2003年国际主要分子生物学数据库
丁香园论坛
20771
2003年国际主要分子生物学数据库
l Major sequence repositories
1. DNA Data Bank of Japan (DDBJ)
http://www.ddbj.nig.ac.jp/
2. EMBL Nucleotide Sequence Database
http://www.ebi.ac.uk/embl.html
3. GenBank
http://www.ncbi.nlm.nih.gov/
4. NCBI Reference Sequence Project
http://www.ncbi.nlm.nih.gov/RefSeq/
Non-redundant collection of naturallyoccurring biological molecules
5. Ensembl
http://www.ensembl.org/
Annotated information on eukaryotic genomes
6. UCSC Genome Browser
http://genome.ucsc.edu/
Genome assemblies and annotation
7. STACK
http://www.sanbi.ac.za/Dbases.html
Non-redundant, gene-oriented clusters
8. TIGR Gene Indices
http://www.tigr.org/tdb/tgi.shtml
Non-redundant, gene-oriented clusters
9. UniGene
http://www.ncbi.nlm.nih.gov/UniGene/
Non-redundant, gene-oriented clusters
l Comparative Genomics
10. Clusters of Orthologous Groups (COG)
http://www.ncbi.nlm.nih.gov/COG
Phylogenetic classification of proteins from 43 complete genomes
11. CORG
http://corg.molgen.mpg.de/
Conserved non-coding sequence blocks
12. Homophila
http://homophila.sdsc.edu/
Relationship of human disease genes to genes in Drosophila
13. MBGD
http://mbgd.genome.ad.jp/
Microbial genome database for comparative genomic analysis
14. ParaDB
http://abi.marseille.inserm.fr/paradb/
Paralogy mapping in human genomes
15. XREFdb
http://www.ncbi.nlm.nih.gov/XREFdb/
Cross-referencing of model organism genetics with mammalian phenotypes
l Gene Expression
16. ArrayExpress
http://www.ebi.ac.uk/arrayexpress
Public collection of microarray gene expression data
17. Axeldb
http://www.dkfz-heidelberg.de/abt0135/axeldb.htm
Gene expression in Xenopus
18. BodyMap
http://bodymap.ims.u-tokyo.ac.jp/
Human and mouse gene expression data
19. EPConDB
http://www.cbil.upenn.edu/EPConDB
Endocrine pancreas consortium database
20. FlyView
http://pbio07.uni-muenster.de/
Drosophila development and genetics
21. Gene Expression Database (GXD)
http://www.informatics.jax.org/menus/expression_menu.shtml
Mouse gene expression and genomics
22. HugeIndex
http://hugeindex.org/
mRNA expression levels of human genes in normal tissues
23. Interferon_Stimulated_Gene_Database
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi
Genes induced by treatment with interferons
24. Kidney Development Database
http://golgi.ana.ed.ac.uk/kidhome.html
Kidney development and gene expression
25. MAGEST
http://www.genome.ad.jp/magest
Ascidian (Halocynthia roretzi) gene expression patterns
26. MEPD
http://medaka.dsp.jst.go.jp/MEPD
Gene expression data from the small freshwater fish Medaka (Oryzias latipes)
27. MethDB
http://www.methdb.de/
DNA methylation data, patterns and profiles
28. Mouse Atlas and Gene Expression Database
http://genex.hgu.mrc.ac.uk/
Spatially-mapped gene expression data
29. MTID
http://mouse.ccgb.umn.edu/transposon/
Sleeping beauty transposon insertions in mice
30. NetAffx
http://www.affymetrix.com/
Public Affymetrix probesets and annotations
31. RECODE expression
http://recode.genetics.utah.edu/
Genes using programmed translational recoding in their expression
32. SeedGenes
http://www.seedgenes.org/
Genes essential for Arabidopsis development
33. Stanford Microarray Database
http://genome-www.stanford.edu/microarray
Raw and normalized data from microarray experiments
34. Tooth Development Database
http://bite-it.helsinki.fi/
Gene expression in dental tissue
35. TRANSPATH
http://www.biobase.de/pages/products/databases.html
Gene regulatory networks and microarray analysis
36. TRIPLES
http://ygac.med.yale.edu/
TRansposon-insertion phenotypes,localization, and expression
in Saccharomyces
l Gene Identification and Structure
37. AllGenes
http://www.allgenes.org/
Human and mouse gene index integrating gene, transcript and protein annotation
38. Ares Lab Yeast Intron Database
http://www.cse.ucsc.edu/research/compbio/yeast_introns.htmlyeast_introns.html
Splicesomal introns in Saccharomyces cerevisiae
39. ASAP
http://www.bioinformatics.ucla.edu/ASAP
Alternative spliced isoforms
40. CUTG
http://www.kazusa.or.jp/codon/
Codon usage tables
41. DBTBS
http://elmo.ims.u-tokyo.ac.jp/dbtbs/
Bacillus subtilis binding factors and promoters
42. EID
http://mcb.harvard.edu/gilbert/EID/
Protein-coding, intron-containing genes
43. EPD
http://www.epd.isb-sib.ch/
Eukaryotic POL II promoters with experimentally-determined transcription start sites
44. ExInt
http://intron.bic.nus.edu.sg/exint/exint.html
Exon–intron structure of eukaryotic genes
45. Gene Resource Locator
http://grl.gi.k.u-tokyo.ac.jp/
Alignment of ESTs with finished human sequence
46. HS3D
http://www.sci.unisannio.it/docenti/rampone/
Human exon, intron and splice regions
47. HUNT
http://www.hri.co.jp/HUNT
Annotated human full-length cDNA sequences
48. HvrBase
http://www.hvrbase.org/
Primate mtDNA control region sequences
49. IDB/IEDB
http://nutmeg.bio.indiana.edu/intron/index.html
Intron sequence and evolution
50. MICdb
http://www.cdfd.org.in/micas
Prokaryotic microsatellites
51. PACRAT
http://www.biosci.ohio-state.edu/_pacrat
Archaeal and bacterial intergenic sequence features
52. PLACE
http://www.dna.affrc.go.jp/htdocs/PLACE
Plant cis-acting regulatory elements
53. PlantCARE
http://oberon.rug.ac.be:8080/PlantCARE/
Plant cis-acting regulatory elements
54. PlantProm
http://mendel.cs.rhul.ac.uk/
Proximal promoter sequences for RNA polymerase II
55. PromEC
http://bioinfo.md.huji.ac.il/marg/promec
Escherichia coli mRNA promoters with experimentally-identified transcriptional start sites
56. RRNDB
http://rrndb.cme.msu.edu/
Variation in prokaryotic ribosomal RNA operons
57. rSNP Guide
http://util.bionet.nsc.ru/databases/rsnp.html
Single nucleotide polymorphisms in regulatory gene regions
58. RTPrimerDB
http://www.realtimeprimerdatabase.ht.st/
Validated PCR primer and probe sequence records
59. SNP Consortium database
http://snp.cshl.org/
SNP Consortium data
60. SpliceDB
http://genomic.sanger.ac.uk/spldb/SpliceDB.html
Canonical and non-canonical mammalian splice sites
61. Sputnik
http://mips.gsf.de/proj/sputnik
Functional annotation of clustered plant ESTs
62. STRBase
http://www.cstl.nist.gov/div831/strbase/
Short tandem DNA repeats
63. TRANSCompel
http://www.gene-regulation.com/pub/databases.html#transcompel
Composite regulatory elements
64. Transterm
http://uther.otago.ac.nz/Transterm.html
Codon usage, start and stop signals
65. TRRD
http://www.bionet.nsc.ru/trrd/
Transcription regulatory regions of eukaryotic genes
66. VIDA
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
Virus genome open reading frames
67. WormBase
http://www.wormbase.org/
Guide to Caenorhabditis elegans biology
68. YIDB
http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html
Yeast nuclear and mitochondrial intron sequences
l Genetic and Physical Maps
69. DRESH
http://www.tigem.it/LOCAL/drosophila/dros.html
Human cDNA clones homologous to Drosophila mutant genes
70. G3-RH
http://www-shgc.stanford.edu/RH/
Stanford G3 and TNG radiation hybrid maps
71. GB4-RH
http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml
Genebridge4 (GB4) human radiation hybrid maps
72. GDB
http://www.gdb.org/
Human genes and genomic maps
73. GenAtlas
http://www.citi2.fr/GENATLAS/
Human genes, markers and phenotypes
74. GeneMap ’99
http://www.ncbi.nlm.nih.gov/genemap/
International Radiation Mapping Consortium human gene map
75. Genetpig
http://www.infobiogen.fr/services/Genetpig
Comparative mapping in pig (Sus scrofa)
76. GenMapDB
http://genomics.med.upenn.edu/genmapdb
Mapped human BAC clones
77. HuGeMap
http://www.infobiogen.fr/services/Hugemap
Human genome genetic and physical map data
78. IXDB
http://ixdb.mpimg-berlin-dahlem.mpg.de/
Physical maps of human chromosome X
79. RHdb
http://www.ebi.ac.uk/RHdb
Radiation hybrid map data
80. The Unified Database
http://bioinfo.weizmann.ac.il/udb/
Integrated human map
l Genomic Databases
81. ACeDB information
http://www.acedb.org/
Caenorhabditis elegans, Schizosaccharomyces pombe,and human sequences and genomic information
82. AMmtDB
http://bighost.area.ba.cnr.it/mitochondriome
Metazoan mitochondrial genes
83. ArkDB
http://www.thearkdb.org/
Genome databases for farm and other animals
84. ASAP
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
Systematic annotation package for community-based annotation and analysis of genomes
85. BSD
http://bsd.cme.msu.edu/
Comparative data on known biodegradative organisms
86. CATMA
http://www.catma.org/
Arabidopsis gene sequence tags (GSTs)
87. CnidBase
http://www.cnidome.bu.edu/
Cnidarian evolutionary genomics and gene expression
88. Comprehensive Microbial Resource
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl
Completed microbial genomes
89. CropNet
http://ukcrop.net/
Genome mapping in crop plants
90. CroW 21
http://bioinfo.weizmann.ac.il/crow21/
Human chromosome 21 database
91. CyanoBase
http://www.kazusa.or.jp/cyano/
Synechocystis sp. genome
92. EcoGene
http://bmb.med.miami.edu/EcoGene/EcoWeb/
E. coli K-12 sequences
93. EMGlib
http://pbil.univ-lyon1.fr/emglib/emglib.html
Completely-sequenced prokaryotic genomes
94. ERGO
http://ergo.integratedgenomics.com/ERGO
Integrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature
95. FlyBase
http://flybase.bio.indiana.edu/
Drosophila sequences and genomic information
96. Full-Malaria
http://fullmal.ims.u-tokyo.ac.jp/
Full-length cDNA library from erythrocytic-stage Plasmodium falciparum
97. GeneCards
http://bioinfo.weizmann.ac.il/cards/
Integrated database of human genes,maps, proteins and diseases
98. Genew
http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl
Approved symbols for all human genes
99. GOBASE
http://megasun.bch.umontreal.ca/gobase/gobase.html
Organelle genome database
100. GOLD
http://igweb.integratedgenomics.com/GOLD/
Information regarding complete and ongoing genome projects
101. Ge´noPlante-Info
http://genoplante-info.infobiogen.fr/
Plant genomic data derived from the Ge´noplante consortium
102. GrainGenes
http://www.graingenes.org/
Genomic database for small-grain crops
103. HGT-DB
http://www.fut.es/~debb/HGT/
Putative horizontally-transferred genes in prokaryotic genomes
104. HIV Sequence Database
http://hiv-web.lanl.gov/
HIV RNA sequences
105. HOWDY
http://www-alis.tokyo.jst.go.jp/HOWDY/
Integrated human genomic information
106. Human BAC Ends Database
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
Non-redundant human BAC end sequences
107. ICB
http://www.mbio.co.jp/icb
Prokaryotic protein-coding gene data
108. INE
http://rgp.dna.affrc.go.jp/giot/INE.html
Integrated database for rice genome analysis and sequencing
109. IRIS
http://www.iris.irri.org/
Rice germplasm geneology and field data; rice structural and functional genomics and proteomics
110. Medicago Genome Initiative (MGI)
http://xgi.ncgr.org/mgi
Model legume Medicago ESTs, gene expression and proteomic data
111. Mendel Database family
http://www.mendel.ac.uk/
Database of plant EST and STS sequences annotated with gene family information
112. MIPS
http://www.mips.biochem.mpg.de/
Protein and genomic sequences
113. MitBASE
http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl
Mitochondrial genomes, intra-species variants, and mutants
114. MitoDat
http://www-lecb.ncifcrf.gov/mitoDat/
Mitochondrial proteins(predominantly human)
115. MITOMAP
http://www.gen.emory.edu/mitomap.html
Human mitochondrial genome
116. MitoNuc/MitoAln
http://bio-www.ba.cnr.it:8000/BioWWW/#MitoNuc
Nuclear genes coding for mitochondrial proteins
117. MITOP
http://www.mips.biochem.mpg.de/proj/medgen/mitop/
Mitochondrial proteins, genes and diseases
118. MOsDB
http://mips.gsf.de/proj/rice
Oryza sativa genome
119. Mouse Genome Database (MGD)
http://www.informatics.jax.org/
Mouse genetics, genomics, alleles and phenotypes
120. MtDB
http://www.medicago.org/MtDB
Medicago trunculata genome
121. NRSub
http://pbil.univ-lyon1.fr/nrsub/nrsub.html
B. subtilis genome
122. OGRe
http://www.bioinf.man.ac.uk/ogre
Complete mitochondrial genome sequences for 200 metazoan species
123. Oryzabase
http://www.shigen.nig.ac.jp/rice/oryzabase/
Rice genetics and genomics
124. PEDANT genome database
http://pedant.gsf.de/
Automated analysis of genomic sequences
125. Phytophthora Genome Consortium Database
https://xgi.ncgr.org/pgc
ESTs from Phytophthora infestans and Phytophthora sojae
126. PlantGDB
http://zmdb.iastate.edu/PlantGDB/
Actively-transcribed plant genomic sequences
127. PlasmoDB
http://plasmodb.org/
Plasmodium genome
128. Proteome BioKnowledge Library
http://www.proteome.com/
Model organism pathogen, and mammalian proteomes
129. Rat Genome Database
http://rgd.mcw.edu/
Rat genetic and genomic data
130. RiceGAAS
http://RiceGaas.dna.affrc.go.jp/
Rice genome sequence
131. RsGDB
http://www-mmg.med.uth.tmc.edu/
sphaeroides Rhodobacter sphaeroides genome
132. RTPrimerDB
http://www.realtimeprimerdatabase.ht.st/
Real-time PCR primer and probe sequences
133. Saccharomyces Genome Database
http://genome-www.stanford.edu/Saccharomyces/
Saccharomyces cerevisiae genome
134. SOURCE
http://source.stanford.edu/
Functional genomic resource for annotations ontologies, and expression data
135. SubtiList
http://genolist.pasteur.fr/SubtiList/
Bacillus subtilis 168 genome
136. The Arabidopsis Information Resource (TAIR)
http://www.arabidopsis.org/
Arabidopsis thaliana genome
137. TIGR Microbial Database
http://www.tigr.org/tdb/mdb/mdbcomplete.html
Microbial genomes and chromosomes
138. TIGR Rice Genome Annotation Resource
http://www.tigr.org/tdb/e2k1/osa1/
Rice sequence, BAC/PAC clones and related mapping data
139. ToxoDB: The Toxoplasma gondii Genome Database
http://toxodb.org/
Apicomplexan parasite Toxoplasma gondii genome
140. WILMA
http://www.came.sbg.ac.at/wilma/
Caenorhabditis elegans annotation
141. WorfDB
http://worfdb.dfci.harvard.edu/
Caenorhabditis elegans ORFeome
142. WormBase
http://www.wormbase.org/
Genomic data on C. elegans and related nematodes
143. ZFIN
http://zfin.org/
Genetic, genomic and developmental data from zebrafish
144. ZmDB
http://zmdb.iastate.edu/
Maize genome database
l Intermolecular Interactions
145. BIND
http://bind.ca/
Molecular interactions, complexes and pathways
146. Database of Interacting Proteins (DIP)
http://dip.doe-mbi.ucla.edu/
Experimentally-determined protein–protein interactions
147. Database of Ribosomal Crosslinks (DRC)
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
Ribosomal crosslinking data
148. DPInteract
http://arep.med.harvard.edu/dpinteract/
Binding sites for E. coli DNA-binding proteins
149. InterDom
http://interdom.lit.org.sg/
Putative protein domain interactions
150. JenPep
http://www.jenner.ac.uk/Jenpep2
Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules
151. KDBI
http://xin.cz3.nus.edu.sg/group/kdbi.asp
Kinetic data on biomolecular interactions
152. MHC—Peptide Interaction Database
http://surya.bic.nus.edu.sg/mpid
Class I and Class II MHC-peptide complexes
153. STRING
http://www.bork.embl-heidelberg.de/STRING/
Predicted functional associations between proteins
l Metabolic Pathways and Cellular Regulation
154. EcoCyc
http://ecocyc.org/
Escherichia coli K-12 genome, metabolic pathways, transporters and gene regulation
155. ENZYME
http://www.expasy.ch/enzyme/
Enzyme nomenclature
156. EpoDB
http://www.cbil.upenn.edu/EpoDB/
Genes expressed during human erythropoiesis
157. Klotho
http://www.ibc.wustl.edu/klotho/
Collection and categorization of biological compounds
158. Kyoto Encyclopedia of Genes and Genomes (KEGG)
http://www.genome.ad.jp/kegg
Metabolic and regulatory pathways
159. LIGAND
http://www.genome.ad.jp/ligand/
Chemical compounds and reactions in biological pathways
160. MetaCyc
http://ecocyc.org/
Metabolic pathways and enzymesfrom various organisms
161. The University of Minnesota Biocatalysis Biodegradation Database
http://umbbd.ahc.umn.edu/
Curated information on microbial catabolism and related biotransformations
162. PathDB
http://www.ncgr.org/pathdb
Biochemical pathways, compounds and metabolism
163. PRODORIC
http://prodoric.tu-bs.de/
Prokaryotic database of gene regulation and regulatory networks
164. RegulonDB
http://www.cifn.unam.mx/Computational_Genomics/regulondb/
Escherichia coli transcriptional regulation and operon organization
165. UM-BBD
http://umbbd.ahc.umn.edu/
Microbial biocatalytic reactions and biodegradation pathways
166. WIT2
http://wit.mcs.anl.gov/WIT2/
Integrated system for metabolic models
l Mutation Databases
167. ALFRED
http://alfred.med.yale.edu/
Allele frequencies and DNA polymorphisms
168. Androgen Receptor Gene Mutations Database
http://www.mcgill.ca/androgendb/
Mutations in the androgen receptor gene
169. Asthma Gene Database
http://cooke.gsf.de/asthmagen/main.cfm
Linkage and mutation studies on the genetics of asthma and allergy
170. Atlas of Genetics and Cytogenetics in Oncology and Haematology
http://www.infobiogen.fr/services/chromcancer/
Chromosomal abnormalities in oncology and haematology
171. BTKbase
http://bioinf.uta.fi/BTKbase/
Mutation registry for X-linked agammaglobulinemia
172. CASRDB
http://data.mch.mcgill.ca/casrdb/
CASR mutations causing FHH,NSHPT and ADH
173. Database of Germline p53 Mutations
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm
Mutations in human tumor and cell line p53 gene
174. dbSNP
http://www.ncbi.nlm.nih.gov/SNP/
Single nucleotide polymorphisms
175. FLAGdb/FST
http://genoplante-info.infobiogen.fr/
Arabidopsis thaliana T-DNA transformants
176. GRAP Mutant Databases
http://tinyGRAP.uit.no/GRAP/
Mutants of family A G-Protein Coupled Receptors (GRAP)
177. Haemophila B Mutation Database IX
http://www.umds.ac.uk/molgen/haemBdatabase.htm
Point mutations, short additions and deletions in the Factor IX gene
178. HGVbase
http://hgvbase.cgb.ki.se/
Curated human polymorphisms
179. HIV-RT
http://hivdb.stanford.edu/hiv/
HIV reverse transcriptase and protease sequence variation
180. Human Gene Mutation Database (HGMD)
http://www.hgmd.org/
Known (published) gene lesions underlying human inherited disease
181. Human p53/hprt, rodent lacI/lacZ databases
http://www.ibiblio.org/dnam/mainpage.html
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
182. Human PAX2 Allelic Variant Database
http://www.hgu.mrc.ac.uk/Softdata/PAX2/
Mutations in human PAX2 gene
183. Human PAX6 Allelic Variant Database
http://www.hgu.mrc.ac.uk/Softdata/PAX6/
Mutations in human PAX6 gene
184. Human Type I and III Collagen Mutation Database
http://www.le.ac.uk/genetics/collagen/
Human type I and type III collagen gene mutations
185. iARC TP53 Database
http://www.iarc.fr/p53/
Human TP53 somatic and germline mutations
186. KinMutBase
http://www.uta.fi/imt/bioinfo/KinMutBase/
Disease-causing protein kinase mutations
187. Mutation Spectra Database
http://info.med.yale.edu/mutbase/
Mutations in viral, bacterial, yeast and mammalian genes
188. NCL Mutations
http://www.ucl.ac.uk/ncl/
Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
189. Online Mendelian Inheritance in Animals
http://www.angis.org.au/omia
Catalog of animal genetic and genomic disorders
190. Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/Omim/
Catalog of human genetic and genomic disorders
191. PAHdb
http://www.mcgill.ca/pahdb/
Mutations at the phenylalanine hydroxylase locus
192. PHEXdb
http://data.mch.mcgill.ca/phexdb
Mutations in PHEX gene causing X-linked hypophosphatemia
193. PMD
http://pmd.ddbj.nig.ac.jp/
Compilation of protein mutant data
194. PTCH1 Mutation Database
http://www.cybergene.se/PTCH/ptchbase.html
Mutations and SNPs found in PTCH1
195. RB1 Gene Mutation Database
http://www.d-lohmann.de/Rb/
Mutations in the human retinoblastoma (RB1) gene
196. SV40 Large T-Antigen Mutant Database
http://bigdaddy.bio.pitt.edu/SV40/
Mutations in SV40 large tumor antigen gene
l Pathology
197. BayGenomics
http://baygenomics.ucsf.edu/
Identification of genes relevant to cardiovascular and pulmonary disease
198. FIMM
http://sdmc.krdl.org.sg:8080/fimm/
Functional molecular immunology data
199. GOLD.db
http://gold.tugraz.at/
Genes, proteins, and pathways implicated in lipid-associated disorders
200. INFEVERS
http://fmf.igh.cnrs.fr/infevers
Familial Mediterranean Fever and hereditary inflammatory disorder mutation data
201. MetaFMF
http://fmf.igh.cnrs.fr/metaFMF/index_us.html
Familial Mediterranean Fever phenotype-genotype correlation
202. Mouse Tumor Biology Database
203. http://tumor.informatics.jax.org
Mouse tumor names, classification, incidence, pathology, genetic factors
204. Oral Cancer Gene Database
http://www.tumor-gene.org/Oral/oral.html
Cellular, molecular and biological data for genes involved in oral cancer
205. PEDB
http://www.pedb.org/
Sequences from prostate tissue and cell type-specific cDNA libraries
206. PGDB
http://www.ucsf.edu/PGDB
Genes and genomic loci related to the prostate and prostatic diseases
207. Tumor Gene Family Databases (TGDBs)
http://www.tumor-gene.org/tgdf.html
Cellular, molecular and biological data about genes involved in various cancers
l Protein Databases
208. AARSDB
http://rose.man.poznan.pl/aars/index.html
Aminoacyl-tRNA synthetase sequences
209. ABCdb
http://ir2lcb.cnrs-mrs.fr/ABCdb/
ABC transporters
210. AraC/XylS database
http://www.arac-xyls.org/
AraC/XylS protein family of positive regulators in bacteria
211. ASPD
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
Artificial Selected Proteins/Peptides Database
212. CSDBase
http://www.chemie.uni-marburg.de/~csdbase/
Cold shock domain-containing proteins
213. DAtA
http://luggagefast.Stanford.EDU/group/arabprotein/
Annotated coding sequences from Arabidopsis
214. DExH/D Family Database
http://www.helicase.net/dexhd/dbhome.htm
DEAD-box, DEAH-box and DExH-box proteins
215. Endogenous GPCR List
http://www.biomedcomp.com/GPCR.html
G protein-coupled receptors;expression in cell lines
216. ESTHER
http://www.ensam.inra.fr/cholinesterase/
Esterases and alpha/beta hydrolase enzymes and relatives
217. EXProt
http://www.cmbi.nl/exprot
Proteins with experimentally-verified function
218. GenProtEC
http://genprotec.mbl.edu/
E. coli K-12 genome, gene products and homologs
219. GPCRDB
http://www.gpcr.org/7tm/
G protein-coupled receptors
220. Histone Database
http://research.nhgri.nih.gov/histones/
Histone and histone fold sequences and structures
221. HIV Molecular Immunology Database
http://hiv-web.lanl.gov/immunology/
HIV epitopes
222. HIV RT and Protease Sequence Database
http://hivdb.stanford.edu/
HIV reverse transcriptase and protease sequences
223. Homeobox Page
http://www.biosci.ki.se/groups/tbu/homeo.html
Information relevant to homeobox proteins, classification and evolution
224. Homeodomain Resource genomic
http://research.nhgri.nih.gov/homeodomain
Homeodomain sequences, structures and related genetic and genomic information
225. HORDE
http://bioinfo.weizmann.ac.il/HORDE/
Olfactory receptor genes and proteins
226. HUGE
http://www.kazusa.or.jp/huge/
Large (>50 kDa) human proteins and cDNA sequences
227. IMGT
http://imgt.cines.fr/
Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates
228. IMGT/HLA
http://www.ebi.ac.uk/imgt/hla/
Polymorphic sequences of human MHC and related genes
229. IMGT/MHC Database
http://www.ebi.ac.uk/imgt/mhc/
Major histocompatibility complex sequences
230. InBase
http://www.neb.com/neb/inteins.html
All known inteins (protein splicing elements): properties, sequences, bibliography
231. InterPro
http://www.ebi.ac.uk/interpro
Protein families and domains
232. Kabat Database
http://immuno.bme.nwu.edu/
Sequences of proteins of immunological interest
233. LGICdb
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
Ligand-gated ion channel subunit sequences
234. Lipase Engineering Database
http://www.led.uni-stuttgart.de/
Integrated information on sequence, structure and function of lipases and esterases
235. MEROPS
http://www.merops.ac.uk/
Proteolytic enzymes (proteases/peptidases)
236. MetaFam
http://metafam.ahc.umn.edu/
Integrated protein family information
237. Metalloprotein Database and Browser
http://metallo.scripps.edu/
Metal-binding sites in metalloproteins
238. MitoDrome
http://bighost.area.ba.cnr.it/BIG/MitoDrome
Drosophila nuclear genes encoding proteins targeted to the mitochondrion
239. MHCPEP
http://wehih.wehi.edu.au/mhcpep/
MHC-binding peptides
240. MPIMP
http://millar3.biochem.uwa.edu.au/~lister/index.html
Mitochondrial protein import machinery of plants
241. Nuclear Protein Database (NPD)
http://npd.hgu.mrc.ac.uk/
Proteins localized in the nucleus
242. Nuclear Receptor Resource
http://nrr.georgetown.edu/nrr/nrr.html
Nuclear receptor superfamily
243. NRMD
http://www.receptors.org/NR/
Nuclear receptor superfamily
244. NUREBASE
http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
Nuclear hormone receptors
245. Olfactory Receptor Database
http://ycmi.med.yale.edu/senselab/ordb/
Sequences for olfactory receptor-like molecules
246. ooTFD
http://www.ifti.org/
Transcription factors and gene expression
247. PANTHER
http://panther.celera.com/
Gene products organized by biological function
248. Peptaibol
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html
Peptaibol (antibiotic peptide) sequences
249. PhosphoBase
http://www.cbs.dtu.dk/databases/PhosphoBase/
Protein phosphorylation sites
250. PIR-NREF
http://pir.georgetown.edu/pirwww/pirnref.shtml
Non-redundant reference database with comprehensive protein sequences
251. PKR
http://pkr.sdsc.edu/
Protein kinase sequences, enzymology,genetics and molecular and structural properties
252. PLANT-PIs
http://bighost.area.ba.cnr.it/PLANT-PIs
Plant protease inhibitors
253. PlantsP/PlantsT
http://plantsp.sdsc.edu/
Functional geomics databases focusing on protein involved in plant phosphorylation and membrane transport, respectively
254. PPMdb data
http://sphinx.rug.ac.be:8080/ppmdb/index.html
Arabidopsis plasma membrane protein sequence and expression data
255. Prolysis
http://delphi.phys.univ-tours.fr/Prolysis/
Proteases and natural and synthetic protease inhibitors
256. Protein Information Resource (PIR)
http://pir.georgetown.edu/
Comprehensive, annotated, non-redundant protein sequence databases
257. ProtoNet
http://www.protonet.cs.huji.ac.il/
Hierarchical clustering of SWISS-PROT
258. Ribonuclease P Database
http://www.mbio.ncsu.edu/RNaseP/home.html
RNase P sequences, alignments and structures
259. RTKdb
http://pbil.univ-lyon1.fr/RTKdb/
Receptor tyrosine kinase sequences
260. S/MARt dB
http://transfac.gbf.de/SMARtDB/
Nuclear scaffold/matrix attached regions
261. SDAP
http://fermi.utmb.edu/SDAP
Sequences, structures and IgE epitopes of allergenic proteins
262. SENTRA
http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html
Sensory signal transduction proteins
263. SEVENS
http://sevens.cbrc.jp/
7-transmembrane helix receptors
264. SRPDB
http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
Structural and functional information on signal recognition particles
265. SWISS-PROT/TrEMBL
http://www.expasy.ch/sprot
Curated protein sequences
266. TIGRFAMs
http://www.tigr.org/TIGRFAMs
Functional identification of proteins
267. TRANSFAC
http://transfac.gbf.de/TRANSFAC/index.html
Transcription factors and binding sites
268. trEST, trGEN, Hits
http://hits.isb-sib.ch/
Hypothetical protein sequences
269. VIDA
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
Homologous viral protein families
270. Wnt Database
http://www.stanford.edu/~rnusse/wntwindow.html
Wnt proteins and phenotypes
l Protein Sequence Motifs
271. ASC—Active Sequence Collection
http://crisceb.unina2.it/ASC/
Biologically-active short amino acid sequences
272. Blocks
http://blocks.fhcrc.org/
Multiple alignments of conserved regions of protein families
273. CDD
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Alignment models for conserved protein domains
274. CluSTr
http://www.ebi.ac.uk/clustr/
Automatic classification of SWISS-PROT+TrEMBL proteins
275. eMOTIF
http://motif.stanford.edu/emotif
Protein sequence motif determination and searches
276. InterPro domains
http://www.ebi.ac.uk/interpro/
Integrated documentation resource for protein families, domains, and sites
277. iProClass
http://pir.georgetown.edu/iproclass/
Annotated protein database with family,function and structure information
278. NESbase 1.0
http://www.cbs.dtu.dk/databases/NESbase
Nuclear export signals
279. NLSdb
http://cubic.bioc.columbia.edu/db/NLSdb/
Nuclear localization signals
280. GLYCBASE
http://www.cbs.dtu.dk/databases/OGLYCBASE/
O- and C-linked glycosylation sites in proteins
281. Pfam
http://www.sanger.ac.uk/Software/Pfam/
Multiple sequence alignments and hidden Markov models of common protein domains
282. PIR-ALN
http://pir.georgetown.edu/pirwww/dbinfo/piraln.html
Protein sequence alignments
283. PRINTS
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
Hierarchical gene family fingerprints
284. ProClass patterns
http://pir.georgetown.edu/gfserver/proclass.html
Protein families defined by PIR superfamilies and PROSITE patterns
285. ProDom
http://www.toulouse.inra.fr/prodom.html
Protein domain families
286. PROSITE
http://www.expasy.org/prosite
Biologically-significant protein patterns and profiles
287. ProtoMap
http://protomap.cornell.edu/
Automated hierarchical classification of SWISS-PROT proteins
288. SBASE
http://www.icgeb.org/sbase
Protein domain sequences and tools
289. SMART
http://smart.embl-heidelberg.de/
Simple Modular Architecture Research Tool
290. SUPFAM
http://pauling.mbu.iisc.ernet.in/~supfam
Grouping of sequence familieinto superfamilies
291. SYSTERS, GeneNest, SpliceNest
http://cmb.molgen.mpg.de/
Integrated database of protein families, EST clusters and their genomic positions
292. TMPDB
http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
Experimentally-characterized transmembrane topologies
l Proteome Resources
293. AAindex
http://www.genome.ad.jp/aaindex/
Physicochemical and biological properties of amino acids
294. GELBANK
http://gelbank.anl.gov/
2D-gel electrophoresis patterns from completed genomes
295. PEP: Predictions for Entire Proteomes
http://cubic.bioc.columbia.edu/pep/
Summarized analyses of protein sequences
296. Proteome Analysis Database
http://www.ebi.ac.uk/proteome/
Online application of InterPro and cluSTr for the functional classification of proteins in whole genomes
297. REBASE
http://rebase.neb.com/rebase/rebase.html
Restriction enzymes and associated methylases
298. SWISS-2DPAGE
http://www.expasy.org/ch2d/
Annotated two-dimensional polyacrylamide gel electrophoresis Database
l Retrieval Systems and Database Structure
299. TESS
http://www.cbil.upenn.edu/tess
Transcription element search system
300. Virgil
http://www.infobiogen.fr/services/virgil
Database interconnectivity
l RNA Sequences
301. 16S and 23S Ribosomal RNA Mutation Database
http://www.fandm.edu/Departments/Biology/Databases/RNA.html
16S and 23S ribosomal RNA mutations
302. 5S Ribosomal RNA Database
http://biobases.ibch.poznan.pl/5SData/
5S rRNA sequences
303. ACTIVITY
http://util.bionet.nsc.ru/databases/activity.html
Functional DNA/RNA site activity
304. ARED
http://rc.kfshrc.edu.sa/ared
AU-rich element-containing mRNAs
305. Database for mobile group II introns
http://www.fp.ucalgary.ca/group2introns/
Database for mobile group II introns
306. Guide RNA Database
http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
Guide RNA sequences
307. HyPaLib
http://bibiserv.techfak.uni-bielefeld.de/HyPa/
Structural elements characteristic for classes of RNA
308. Intronerator
http://www.cse.ucsc.edu/~kent/intronerator/
RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
309. IRESdb
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
Internal ribosome entry sites
310. NCIR
http://prion.bchs.uh.edu/bp_type/
Non-standard base-base interactions in known RNA structures
311. Noncoding regulatory RNAs database
http://biobases.ibch.poznan.pl/ncRNA/
Noncoding RNAs with regulatory functions
312. PLANTncRNAs
http://www.prl.msu.edu/PLANTncRNAs/
Plant non-protein coding RNAs with relevant gene expression information
313. Plant snoRNA DB
http://www.scri.sari.ac.uk/plant_snoRNA/
snoRNA genes in plant species
314. PLMItRNA
http://bighost.area.ba.cnr.it/PLMItRNA/
Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
315. PseudoBase
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
Structural, functional and sequence data related to RNA pseudoknots
316. Rfam
http://www.sanger.ac.uk/Software/Rfam/
Non-coding RNA families
317. Ribosomal Database Project (RDP-II)
http://rdp.cme.msu.edu/
rRNA sequence data, analysis tools, alignments and phylogenies
318. RISCC
http://ulises.umh.es/RISSC
Ribosomal 16S–23S RNA gene spacer regions
319. RNA Modification Database
http://medlib.med.utah.edu/RNAmods/
Naturally modified nucleosides in RNA
320. SELEXdb
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
Selected DNA/RNA functional site sequences
321. Small RNA Database
http://mbcr.bcm.tmc.edu/smallRNA
Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
322. SRPDB
http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
Signal recognition particle RNA, SRP protein and SRP receptor sequences and alignments
323. Subviral RNA Database
http://penelope.med.usherb.ca/subviral/
Database of viroids and viroid-like RNAs
324. tmRDB
http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
tmRNA (10Sa RNA) sequences and alignments
325. tRNA Sequences
http://www.uni-bayreuth.de/departments/biochemie/trna/
tRNA and tRNA gene sequences
326. tmRNAWebsite
http://www.indiana.edu/~tmrna
tmRNA sequences, foldings, and alignments
327. UTRdb/UTRsite
http://bighost.area.ba.cnr.it/srs6/
5- and 3-UTRs of eukaryotic mRNAs and relevant functional patterns
328. Yeast snoRNA Database
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
Yeast small nucleolar RNAs
l Structure
329. ASTRAL
http://astral.stanford.edu/
Sequences of domains of known structure, selected subsets and sequence-structure correspondences
330. BioMagResBank acids
http://www.bmrb.wisc.edu/
NMR spectroscopic data from proteins peptides, and nucleic acids
331. CADB
http://144.16.71.148/
Conformation angles of protein structures, with associated crystallographic data
332. CATH
http://www.biochem.ucl.ac.uk/bsm/cath_new
Protein domain structures
333. CE
http://cl.sdsc.edu/ce.html
CE: a resource to compute and review 3D protein structure alignments
334. CKAAPs DB
http://ckaap.sdsc.edu/
Structurally-similar proteins with dissimilar sequences
335. CSD
http://www.ccdc.cam.ac.uk/prods/csd/csd.html
Crystal structure information for organic and metal organic compounds
336. Database of Macromolecular Movements
http://bioinfo.mbb.yale.edu/MolMovDB/
Descriptions of protein and macromolecular motions, including movies
337. Decoys ‘R’ Us
http://dd.stanford.edu/
Computer-generated protein conformations based on sequence data
338. DSDBASE
http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
Native and modeled disulfide bonds in proteins
339. DSMM
http://projects.eml.org/mcm/database/dsmm
Database of Simulated Molecular Motions
340. E-MSD
http://www.ebi.ac.uk/msd
Collected data on macromolecular structures
341. FAMSBASE
http://famsbase.bio.nagoya-u.ac.jp/famsbase/
Protein three-dimensional structural models
342. Gene3D
http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
Precalculated structural assignments for genes within whole genomes
343. GTOP
http://spock.genes.nig.ac.jp/~genome/gtop.html
Protein fold predictions from genome sequences
344. HIC-Up
http://alpha2.bmc.uu.se/hicup/
Structures of small molecules (‘hetero-compounds’)
345. HSSP
http://www.sander.ebi.ac.uk/hssp/
Structural families and alignments; structurarlly-conserved regions and domain architecture
346. IMB Jena Image Library of Biological Macromolecules
http://www.imb-jena.de/IMAGE.html
Visualization and analysis of three-dimensional biopolymer structures
347. ISSD
http://www.protein.bio.msu.su/issd/
Integrated sequence and structural information
348. LPFC
http://www-smi.stanford.edu/projects/helix/LPFC/
Library of protein family core structures
349. MMDB linked
http://www.ncbi.nlm.nih.gov/Structure/
All experimentally-determined three-dimensional structures, linked to NCBI Entrez
350. MolMovDB
http://molmovdb.org/
Database of macromolecular movements
351. ModBase
http://guitar.rockefeller.edu/modbase
Annotated comparative protein structure models
352. NDB
http://ndbserver.rutgers.edu/
Nucleic acid-containing structures
353. NTDB
http://ntdb.chem.cuhk.edu.hk/
Thermodynamic data for nucleic acids
354. PALI
http://pauling.mbu.iisc.ernet.in/~pali
Phylogeny and alignment of homologous protein structures
355. PASS2
http://ncbs.res.in/~faculty/mini/campass/pass.html
Structural motifs of protein superfamilies
356. PDB
http://www.pdb.org/
Structure data determined by X-raycryst allography and NMR
357. PDB-REPRDB
http://www.cbrc.jp/pdbreprdb/
Representative protein chains, based on PDB entries
358. PDBsum
http://www.biochem.ucl.ac.uk/bsm/pdbsum
Summaries and analyses of PDB structures
359. PRESAGE
http://presage.berkeley.edu/
Protein structures with experimental and predictive annotations
360. ProTherm
http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html
Thermodynamic data for wild-type and mutant proteins
361. PSSH
http://srs3d.ebi.ac.uk/
Alignments between protein sequences and tertiary structures
362. RESID
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html
Protein structure modifications
363. RNABase
http://www.rnabase.org/
RNA-containing structures from PDB and NDB
364. SCOP
http://scop.mrc-lmb.cam.ac.uk/scop
Familial and structural protein relationships
365. SCOR
http://scor.lbl.gov/
RNA structural relationships
366. Sloop
http://www-cryst.bioc.cam.ac.uk/~sloop/
Classification of protein loops
367. Structure-Superposition Database
http://ssd.rbvi.ucsf.edu/
Pairwise superposition of TIM-barrel structures
368. SUPERFAMILY
http://supfam.org/
Assignments of proteins to structural superfamilies
l Transgenics
369. Cre Transgenic Database
http://www.mshri.on.ca/nagy/cre.htm
Cre transgenic mouse lines
370. Transgenic/Targeted Mutation Database
http://tbase.jax.org/
Information on transgenic animals and targeted mutations
l Varied Biomedical Content
371. BAliBASE alignments
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
Benchmark database for comparison of multiple sequence alignments
372. Cytokine Gene Polymorphism in Human Disease
http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm
Cytokine gene polymorphism literature database
373. DBcat
http://www.infobiogen.fr/services/dbcat/
Catalog of databases
374. Global Image Database
http://www.gwer.ch/qv/gid/gid.htm
Annotated biological images
375. GlycoSuiteDB
http://www.glycosuite.com/
N- and O-linked glycan structures and biological source information
376. Imprinted Genes and Parent-of-Origin Effects
http://www.otago.ac.nz/IGC
Imprinted genes and parent-of-origin effects in animals
377. MPDB
http://www.biotech.ist.unige.it/interlab/mpdb.html
Information on synthetic oligonucleotides proven useful as primers or probes
378. NCBI Taxonomy Browser
http://www.ncbi.nlm.nih.gov/Taxonomy/
Names of all organisms that are represented in the genetic databases with at least one nucleotide orprotein sequence
379. probeBase
http://www.probebase.net/
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information
380. PubMed
http://www.ncbi.nlm.nih.gov/PubMed/
MEDLINE and Pre-MEDLINE citations
381. RefSeq
http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html
Reference sequence standards for genomes, genes, transcripts and proteins
382. RIDOM
http://www.ridom.de/
rRNA (16S and ITS) sequence-based identification of medical microorganisms
383. SWEET-DB
http://www.dkfz-heidelberg.de/spec2/sweetdb/
Annotated carbohydrate structure and substance information
The Pharmacogenomics and Pharmacogenetics
384. Knowledge Base
http://www.pharmgkb.org/
Variation in drug response based on human variation
385. Tree of Life
http://phylogeny.arizona.edu/tree/phylogeny.html
Information on phylogeny and biodiversity
386. Vectordb
http://www.atcg.com/vectordb/
Characterization and classification of nucleic acid vectors
387. VirOligo
http://viroligo.okstate.edu/
Virus-specific oligonucleotides for PCR and hybridization
l Major sequence repositories
1. DNA Data Bank of Japan (DDBJ)
http://www.ddbj.nig.ac.jp/
2. EMBL Nucleotide Sequence Database
http://www.ebi.ac.uk/embl.html
3. GenBank
http://www.ncbi.nlm.nih.gov/
4. NCBI Reference Sequence Project
http://www.ncbi.nlm.nih.gov/RefSeq/
Non-redundant collection of naturallyoccurring biological molecules
5. Ensembl
http://www.ensembl.org/
Annotated information on eukaryotic genomes
6. UCSC Genome Browser
http://genome.ucsc.edu/
Genome assemblies and annotation
7. STACK
http://www.sanbi.ac.za/Dbases.html
Non-redundant, gene-oriented clusters
8. TIGR Gene Indices
http://www.tigr.org/tdb/tgi.shtml
Non-redundant, gene-oriented clusters
9. UniGene
http://www.ncbi.nlm.nih.gov/UniGene/
Non-redundant, gene-oriented clusters
l Comparative Genomics
10. Clusters of Orthologous Groups (COG)
http://www.ncbi.nlm.nih.gov/COG
Phylogenetic classification of proteins from 43 complete genomes
11. CORG
http://corg.molgen.mpg.de/
Conserved non-coding sequence blocks
12. Homophila
http://homophila.sdsc.edu/
Relationship of human disease genes to genes in Drosophila
13. MBGD
http://mbgd.genome.ad.jp/
Microbial genome database for comparative genomic analysis
14. ParaDB
http://abi.marseille.inserm.fr/paradb/
Paralogy mapping in human genomes
15. XREFdb
http://www.ncbi.nlm.nih.gov/XREFdb/
Cross-referencing of model organism genetics with mammalian phenotypes
l Gene Expression
16. ArrayExpress
http://www.ebi.ac.uk/arrayexpress
Public collection of microarray gene expression data
17. Axeldb
http://www.dkfz-heidelberg.de/abt0135/axeldb.htm
Gene expression in Xenopus
18. BodyMap
http://bodymap.ims.u-tokyo.ac.jp/
Human and mouse gene expression data
19. EPConDB
http://www.cbil.upenn.edu/EPConDB
Endocrine pancreas consortium database
20. FlyView
http://pbio07.uni-muenster.de/
Drosophila development and genetics
21. Gene Expression Database (GXD)
http://www.informatics.jax.org/menus/expression_menu.shtml
Mouse gene expression and genomics
22. HugeIndex
http://hugeindex.org/
mRNA expression levels of human genes in normal tissues
23. Interferon_Stimulated_Gene_Database
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi
Genes induced by treatment with interferons
24. Kidney Development Database
http://golgi.ana.ed.ac.uk/kidhome.html
Kidney development and gene expression
25. MAGEST
http://www.genome.ad.jp/magest
Ascidian (Halocynthia roretzi) gene expression patterns
26. MEPD
http://medaka.dsp.jst.go.jp/MEPD
Gene expression data from the small freshwater fish Medaka (Oryzias latipes)
27. MethDB
http://www.methdb.de/
DNA methylation data, patterns and profiles
28. Mouse Atlas and Gene Expression Database
http://genex.hgu.mrc.ac.uk/
Spatially-mapped gene expression data
29. MTID
http://mouse.ccgb.umn.edu/transposon/
Sleeping beauty transposon insertions in mice
30. NetAffx
http://www.affymetrix.com/
Public Affymetrix probesets and annotations
31. RECODE expression
http://recode.genetics.utah.edu/
Genes using programmed translational recoding in their expression
32. SeedGenes
http://www.seedgenes.org/
Genes essential for Arabidopsis development
33. Stanford Microarray Database
http://genome-www.stanford.edu/microarray
Raw and normalized data from microarray experiments
34. Tooth Development Database
http://bite-it.helsinki.fi/
Gene expression in dental tissue
35. TRANSPATH
http://www.biobase.de/pages/products/databases.html
Gene regulatory networks and microarray analysis
36. TRIPLES
http://ygac.med.yale.edu/
TRansposon-insertion phenotypes,localization, and expression
in Saccharomyces
l Gene Identification and Structure
37. AllGenes
http://www.allgenes.org/
Human and mouse gene index integrating gene, transcript and protein annotation
38. Ares Lab Yeast Intron Database
http://www.cse.ucsc.edu/research/compbio/yeast_introns.htmlyeast_introns.html
Splicesomal introns in Saccharomyces cerevisiae
39. ASAP
http://www.bioinformatics.ucla.edu/ASAP
Alternative spliced isoforms
40. CUTG
http://www.kazusa.or.jp/codon/
Codon usage tables
41. DBTBS
http://elmo.ims.u-tokyo.ac.jp/dbtbs/
Bacillus subtilis binding factors and promoters
42. EID
http://mcb.harvard.edu/gilbert/EID/
Protein-coding, intron-containing genes
43. EPD
http://www.epd.isb-sib.ch/
Eukaryotic POL II promoters with experimentally-determined transcription start sites
44. ExInt
http://intron.bic.nus.edu.sg/exint/exint.html
Exon–intron structure of eukaryotic genes
45. Gene Resource Locator
http://grl.gi.k.u-tokyo.ac.jp/
Alignment of ESTs with finished human sequence
46. HS3D
http://www.sci.unisannio.it/docenti/rampone/
Human exon, intron and splice regions
47. HUNT
http://www.hri.co.jp/HUNT
Annotated human full-length cDNA sequences
48. HvrBase
http://www.hvrbase.org/
Primate mtDNA control region sequences
49. IDB/IEDB
http://nutmeg.bio.indiana.edu/intron/index.html
Intron sequence and evolution
50. MICdb
http://www.cdfd.org.in/micas
Prokaryotic microsatellites
51. PACRAT
http://www.biosci.ohio-state.edu/_pacrat
Archaeal and bacterial intergenic sequence features
52. PLACE
http://www.dna.affrc.go.jp/htdocs/PLACE
Plant cis-acting regulatory elements
53. PlantCARE
http://oberon.rug.ac.be:8080/PlantCARE/
Plant cis-acting regulatory elements
54. PlantProm
http://mendel.cs.rhul.ac.uk/
Proximal promoter sequences for RNA polymerase II
55. PromEC
http://bioinfo.md.huji.ac.il/marg/promec
Escherichia coli mRNA promoters with experimentally-identified transcriptional start sites
56. RRNDB
http://rrndb.cme.msu.edu/
Variation in prokaryotic ribosomal RNA operons
57. rSNP Guide
http://util.bionet.nsc.ru/databases/rsnp.html
Single nucleotide polymorphisms in regulatory gene regions
58. RTPrimerDB
http://www.realtimeprimerdatabase.ht.st/
Validated PCR primer and probe sequence records
59. SNP Consortium database
http://snp.cshl.org/
SNP Consortium data
60. SpliceDB
http://genomic.sanger.ac.uk/spldb/SpliceDB.html
Canonical and non-canonical mammalian splice sites
61. Sputnik
http://mips.gsf.de/proj/sputnik
Functional annotation of clustered plant ESTs
62. STRBase
http://www.cstl.nist.gov/div831/strbase/
Short tandem DNA repeats
63. TRANSCompel
http://www.gene-regulation.com/pub/databases.html#transcompel
Composite regulatory elements
64. Transterm
http://uther.otago.ac.nz/Transterm.html
Codon usage, start and stop signals
65. TRRD
http://www.bionet.nsc.ru/trrd/
Transcription regulatory regions of eukaryotic genes
66. VIDA
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
Virus genome open reading frames
67. WormBase
http://www.wormbase.org/
Guide to Caenorhabditis elegans biology
68. YIDB
http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html
Yeast nuclear and mitochondrial intron sequences
l Genetic and Physical Maps
69. DRESH
http://www.tigem.it/LOCAL/drosophila/dros.html
Human cDNA clones homologous to Drosophila mutant genes
70. G3-RH
http://www-shgc.stanford.edu/RH/
Stanford G3 and TNG radiation hybrid maps
71. GB4-RH
http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml
Genebridge4 (GB4) human radiation hybrid maps
72. GDB
http://www.gdb.org/
Human genes and genomic maps
73. GenAtlas
http://www.citi2.fr/GENATLAS/
Human genes, markers and phenotypes
74. GeneMap ’99
http://www.ncbi.nlm.nih.gov/genemap/
International Radiation Mapping Consortium human gene map
75. Genetpig
http://www.infobiogen.fr/services/Genetpig
Comparative mapping in pig (Sus scrofa)
76. GenMapDB
http://genomics.med.upenn.edu/genmapdb
Mapped human BAC clones
77. HuGeMap
http://www.infobiogen.fr/services/Hugemap
Human genome genetic and physical map data
78. IXDB
http://ixdb.mpimg-berlin-dahlem.mpg.de/
Physical maps of human chromosome X
79. RHdb
http://www.ebi.ac.uk/RHdb
Radiation hybrid map data
80. The Unified Database
http://bioinfo.weizmann.ac.il/udb/
Integrated human map
l Genomic Databases
81. ACeDB information
http://www.acedb.org/
Caenorhabditis elegans, Schizosaccharomyces pombe,and human sequences and genomic information
82. AMmtDB
http://bighost.area.ba.cnr.it/mitochondriome
Metazoan mitochondrial genes
83. ArkDB
http://www.thearkdb.org/
Genome databases for farm and other animals
84. ASAP
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
Systematic annotation package for community-based annotation and analysis of genomes
85. BSD
http://bsd.cme.msu.edu/
Comparative data on known biodegradative organisms
86. CATMA
http://www.catma.org/
Arabidopsis gene sequence tags (GSTs)
87. CnidBase
http://www.cnidome.bu.edu/
Cnidarian evolutionary genomics and gene expression
88. Comprehensive Microbial Resource
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl
Completed microbial genomes
89. CropNet
http://ukcrop.net/
Genome mapping in crop plants
90. CroW 21
http://bioinfo.weizmann.ac.il/crow21/
Human chromosome 21 database
91. CyanoBase
http://www.kazusa.or.jp/cyano/
Synechocystis sp. genome
92. EcoGene
http://bmb.med.miami.edu/EcoGene/EcoWeb/
E. coli K-12 sequences
93. EMGlib
http://pbil.univ-lyon1.fr/emglib/emglib.html
Completely-sequenced prokaryotic genomes
94. ERGO
http://ergo.integratedgenomics.com/ERGO
Integrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature
95. FlyBase
http://flybase.bio.indiana.edu/
Drosophila sequences and genomic information
96. Full-Malaria
http://fullmal.ims.u-tokyo.ac.jp/
Full-length cDNA library from erythrocytic-stage Plasmodium falciparum
97. GeneCards
http://bioinfo.weizmann.ac.il/cards/
Integrated database of human genes,maps, proteins and diseases
98. Genew
http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl
Approved symbols for all human genes
99. GOBASE
http://megasun.bch.umontreal.ca/gobase/gobase.html
Organelle genome database
100. GOLD
http://igweb.integratedgenomics.com/GOLD/
Information regarding complete and ongoing genome projects
101. Ge´noPlante-Info
http://genoplante-info.infobiogen.fr/
Plant genomic data derived from the Ge´noplante consortium
102. GrainGenes
http://www.graingenes.org/
Genomic database for small-grain crops
103. HGT-DB
http://www.fut.es/~debb/HGT/
Putative horizontally-transferred genes in prokaryotic genomes
104. HIV Sequence Database
http://hiv-web.lanl.gov/
HIV RNA sequences
105. HOWDY
http://www-alis.tokyo.jst.go.jp/HOWDY/
Integrated human genomic information
106. Human BAC Ends Database
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html
Non-redundant human BAC end sequences
107. ICB
http://www.mbio.co.jp/icb
Prokaryotic protein-coding gene data
108. INE
http://rgp.dna.affrc.go.jp/giot/INE.html
Integrated database for rice genome analysis and sequencing
109. IRIS
http://www.iris.irri.org/
Rice germplasm geneology and field data; rice structural and functional genomics and proteomics
110. Medicago Genome Initiative (MGI)
http://xgi.ncgr.org/mgi
Model legume Medicago ESTs, gene expression and proteomic data
111. Mendel Database family
http://www.mendel.ac.uk/
Database of plant EST and STS sequences annotated with gene family information
112. MIPS
http://www.mips.biochem.mpg.de/
Protein and genomic sequences
113. MitBASE
http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl
Mitochondrial genomes, intra-species variants, and mutants
114. MitoDat
http://www-lecb.ncifcrf.gov/mitoDat/
Mitochondrial proteins(predominantly human)
115. MITOMAP
http://www.gen.emory.edu/mitomap.html
Human mitochondrial genome
116. MitoNuc/MitoAln
http://bio-www.ba.cnr.it:8000/BioWWW/#MitoNuc
Nuclear genes coding for mitochondrial proteins
117. MITOP
http://www.mips.biochem.mpg.de/proj/medgen/mitop/
Mitochondrial proteins, genes and diseases
118. MOsDB
http://mips.gsf.de/proj/rice
Oryza sativa genome
119. Mouse Genome Database (MGD)
http://www.informatics.jax.org/
Mouse genetics, genomics, alleles and phenotypes
120. MtDB
http://www.medicago.org/MtDB
Medicago trunculata genome
121. NRSub
http://pbil.univ-lyon1.fr/nrsub/nrsub.html
B. subtilis genome
122. OGRe
http://www.bioinf.man.ac.uk/ogre
Complete mitochondrial genome sequences for 200 metazoan species
123. Oryzabase
http://www.shigen.nig.ac.jp/rice/oryzabase/
Rice genetics and genomics
124. PEDANT genome database
http://pedant.gsf.de/
Automated analysis of genomic sequences
125. Phytophthora Genome Consortium Database
https://xgi.ncgr.org/pgc
ESTs from Phytophthora infestans and Phytophthora sojae
126. PlantGDB
http://zmdb.iastate.edu/PlantGDB/
Actively-transcribed plant genomic sequences
127. PlasmoDB
http://plasmodb.org/
Plasmodium genome
128. Proteome BioKnowledge Library
http://www.proteome.com/
Model organism pathogen, and mammalian proteomes
129. Rat Genome Database
http://rgd.mcw.edu/
Rat genetic and genomic data
130. RiceGAAS
http://RiceGaas.dna.affrc.go.jp/
Rice genome sequence
131. RsGDB
http://www-mmg.med.uth.tmc.edu/
sphaeroides Rhodobacter sphaeroides genome
132. RTPrimerDB
http://www.realtimeprimerdatabase.ht.st/
Real-time PCR primer and probe sequences
133. Saccharomyces Genome Database
http://genome-www.stanford.edu/Saccharomyces/
Saccharomyces cerevisiae genome
134. SOURCE
http://source.stanford.edu/
Functional genomic resource for annotations ontologies, and expression data
135. SubtiList
http://genolist.pasteur.fr/SubtiList/
Bacillus subtilis 168 genome
136. The Arabidopsis Information Resource (TAIR)
http://www.arabidopsis.org/
Arabidopsis thaliana genome
137. TIGR Microbial Database
http://www.tigr.org/tdb/mdb/mdbcomplete.html
Microbial genomes and chromosomes
138. TIGR Rice Genome Annotation Resource
http://www.tigr.org/tdb/e2k1/osa1/
Rice sequence, BAC/PAC clones and related mapping data
139. ToxoDB: The Toxoplasma gondii Genome Database
http://toxodb.org/
Apicomplexan parasite Toxoplasma gondii genome
140. WILMA
http://www.came.sbg.ac.at/wilma/
Caenorhabditis elegans annotation
141. WorfDB
http://worfdb.dfci.harvard.edu/
Caenorhabditis elegans ORFeome
142. WormBase
http://www.wormbase.org/
Genomic data on C. elegans and related nematodes
143. ZFIN
http://zfin.org/
Genetic, genomic and developmental data from zebrafish
144. ZmDB
http://zmdb.iastate.edu/
Maize genome database
l Intermolecular Interactions
145. BIND
http://bind.ca/
Molecular interactions, complexes and pathways
146. Database of Interacting Proteins (DIP)
http://dip.doe-mbi.ucla.edu/
Experimentally-determined protein–protein interactions
147. Database of Ribosomal Crosslinks (DRC)
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
Ribosomal crosslinking data
148. DPInteract
http://arep.med.harvard.edu/dpinteract/
Binding sites for E. coli DNA-binding proteins
149. InterDom
http://interdom.lit.org.sg/
Putative protein domain interactions
150. JenPep
http://www.jenner.ac.uk/Jenpep2
Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules
151. KDBI
http://xin.cz3.nus.edu.sg/group/kdbi.asp
Kinetic data on biomolecular interactions
152. MHC—Peptide Interaction Database
http://surya.bic.nus.edu.sg/mpid
Class I and Class II MHC-peptide complexes
153. STRING
http://www.bork.embl-heidelberg.de/STRING/
Predicted functional associations between proteins
l Metabolic Pathways and Cellular Regulation
154. EcoCyc
http://ecocyc.org/
Escherichia coli K-12 genome, metabolic pathways, transporters and gene regulation
155. ENZYME
http://www.expasy.ch/enzyme/
Enzyme nomenclature
156. EpoDB
http://www.cbil.upenn.edu/EpoDB/
Genes expressed during human erythropoiesis
157. Klotho
http://www.ibc.wustl.edu/klotho/
Collection and categorization of biological compounds
158. Kyoto Encyclopedia of Genes and Genomes (KEGG)
http://www.genome.ad.jp/kegg
Metabolic and regulatory pathways
159. LIGAND
http://www.genome.ad.jp/ligand/
Chemical compounds and reactions in biological pathways
160. MetaCyc
http://ecocyc.org/
Metabolic pathways and enzymesfrom various organisms
161. The University of Minnesota Biocatalysis Biodegradation Database
http://umbbd.ahc.umn.edu/
Curated information on microbial catabolism and related biotransformations
162. PathDB
http://www.ncgr.org/pathdb
Biochemical pathways, compounds and metabolism
163. PRODORIC
http://prodoric.tu-bs.de/
Prokaryotic database of gene regulation and regulatory networks
164. RegulonDB
http://www.cifn.unam.mx/Computational_Genomics/regulondb/
Escherichia coli transcriptional regulation and operon organization
165. UM-BBD
http://umbbd.ahc.umn.edu/
Microbial biocatalytic reactions and biodegradation pathways
166. WIT2
http://wit.mcs.anl.gov/WIT2/
Integrated system for metabolic models
l Mutation Databases
167. ALFRED
http://alfred.med.yale.edu/
Allele frequencies and DNA polymorphisms
168. Androgen Receptor Gene Mutations Database
http://www.mcgill.ca/androgendb/
Mutations in the androgen receptor gene
169. Asthma Gene Database
http://cooke.gsf.de/asthmagen/main.cfm
Linkage and mutation studies on the genetics of asthma and allergy
170. Atlas of Genetics and Cytogenetics in Oncology and Haematology
http://www.infobiogen.fr/services/chromcancer/
Chromosomal abnormalities in oncology and haematology
171. BTKbase
http://bioinf.uta.fi/BTKbase/
Mutation registry for X-linked agammaglobulinemia
172. CASRDB
http://data.mch.mcgill.ca/casrdb/
CASR mutations causing FHH,NSHPT and ADH
173. Database of Germline p53 Mutations
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm
Mutations in human tumor and cell line p53 gene
174. dbSNP
http://www.ncbi.nlm.nih.gov/SNP/
Single nucleotide polymorphisms
175. FLAGdb/FST
http://genoplante-info.infobiogen.fr/
Arabidopsis thaliana T-DNA transformants
176. GRAP Mutant Databases
http://tinyGRAP.uit.no/GRAP/
Mutants of family A G-Protein Coupled Receptors (GRAP)
177. Haemophila B Mutation Database IX
http://www.umds.ac.uk/molgen/haemBdatabase.htm
Point mutations, short additions and deletions in the Factor IX gene
178. HGVbase
http://hgvbase.cgb.ki.se/
Curated human polymorphisms
179. HIV-RT
http://hivdb.stanford.edu/hiv/
HIV reverse transcriptase and protease sequence variation
180. Human Gene Mutation Database (HGMD)
http://www.hgmd.org/
Known (published) gene lesions underlying human inherited disease
181. Human p53/hprt, rodent lacI/lacZ databases
http://www.ibiblio.org/dnam/mainpage.html
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
182. Human PAX2 Allelic Variant Database
http://www.hgu.mrc.ac.uk/Softdata/PAX2/
Mutations in human PAX2 gene
183. Human PAX6 Allelic Variant Database
http://www.hgu.mrc.ac.uk/Softdata/PAX6/
Mutations in human PAX6 gene
184. Human Type I and III Collagen Mutation Database
http://www.le.ac.uk/genetics/collagen/
Human type I and type III collagen gene mutations
185. iARC TP53 Database
http://www.iarc.fr/p53/
Human TP53 somatic and germline mutations
186. KinMutBase
http://www.uta.fi/imt/bioinfo/KinMutBase/
Disease-causing protein kinase mutations
187. Mutation Spectra Database
http://info.med.yale.edu/mutbase/
Mutations in viral, bacterial, yeast and mammalian genes
188. NCL Mutations
http://www.ucl.ac.uk/ncl/
Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
189. Online Mendelian Inheritance in Animals
http://www.angis.org.au/omia
Catalog of animal genetic and genomic disorders
190. Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/Omim/
Catalog of human genetic and genomic disorders
191. PAHdb
http://www.mcgill.ca/pahdb/
Mutations at the phenylalanine hydroxylase locus
192. PHEXdb
http://data.mch.mcgill.ca/phexdb
Mutations in PHEX gene causing X-linked hypophosphatemia
193. PMD
http://pmd.ddbj.nig.ac.jp/
Compilation of protein mutant data
194. PTCH1 Mutation Database
http://www.cybergene.se/PTCH/ptchbase.html
Mutations and SNPs found in PTCH1
195. RB1 Gene Mutation Database
http://www.d-lohmann.de/Rb/
Mutations in the human retinoblastoma (RB1) gene
196. SV40 Large T-Antigen Mutant Database
http://bigdaddy.bio.pitt.edu/SV40/
Mutations in SV40 large tumor antigen gene
l Pathology
197. BayGenomics
http://baygenomics.ucsf.edu/
Identification of genes relevant to cardiovascular and pulmonary disease
198. FIMM
http://sdmc.krdl.org.sg:8080/fimm/
Functional molecular immunology data
199. GOLD.db
http://gold.tugraz.at/
Genes, proteins, and pathways implicated in lipid-associated disorders
200. INFEVERS
http://fmf.igh.cnrs.fr/infevers
Familial Mediterranean Fever and hereditary inflammatory disorder mutation data
201. MetaFMF
http://fmf.igh.cnrs.fr/metaFMF/index_us.html
Familial Mediterranean Fever phenotype-genotype correlation
202. Mouse Tumor Biology Database
203. http://tumor.informatics.jax.org
Mouse tumor names, classification, incidence, pathology, genetic factors
204. Oral Cancer Gene Database
http://www.tumor-gene.org/Oral/oral.html
Cellular, molecular and biological data for genes involved in oral cancer
205. PEDB
http://www.pedb.org/
Sequences from prostate tissue and cell type-specific cDNA libraries
206. PGDB
http://www.ucsf.edu/PGDB
Genes and genomic loci related to the prostate and prostatic diseases
207. Tumor Gene Family Databases (TGDBs)
http://www.tumor-gene.org/tgdf.html
Cellular, molecular and biological data about genes involved in various cancers
l Protein Databases
208. AARSDB
http://rose.man.poznan.pl/aars/index.html
Aminoacyl-tRNA synthetase sequences
209. ABCdb
http://ir2lcb.cnrs-mrs.fr/ABCdb/
ABC transporters
210. AraC/XylS database
http://www.arac-xyls.org/
AraC/XylS protein family of positive regulators in bacteria
211. ASPD
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
Artificial Selected Proteins/Peptides Database
212. CSDBase
http://www.chemie.uni-marburg.de/~csdbase/
Cold shock domain-containing proteins
213. DAtA
http://luggagefast.Stanford.EDU/group/arabprotein/
Annotated coding sequences from Arabidopsis
214. DExH/D Family Database
http://www.helicase.net/dexhd/dbhome.htm
DEAD-box, DEAH-box and DExH-box proteins
215. Endogenous GPCR List
http://www.biomedcomp.com/GPCR.html
G protein-coupled receptors;expression in cell lines
216. ESTHER
http://www.ensam.inra.fr/cholinesterase/
Esterases and alpha/beta hydrolase enzymes and relatives
217. EXProt
http://www.cmbi.nl/exprot
Proteins with experimentally-verified function
218. GenProtEC
http://genprotec.mbl.edu/
E. coli K-12 genome, gene products and homologs
219. GPCRDB
http://www.gpcr.org/7tm/
G protein-coupled receptors
220. Histone Database
http://research.nhgri.nih.gov/histones/
Histone and histone fold sequences and structures
221. HIV Molecular Immunology Database
http://hiv-web.lanl.gov/immunology/
HIV epitopes
222. HIV RT and Protease Sequence Database
http://hivdb.stanford.edu/
HIV reverse transcriptase and protease sequences
223. Homeobox Page
http://www.biosci.ki.se/groups/tbu/homeo.html
Information relevant to homeobox proteins, classification and evolution
224. Homeodomain Resource genomic
http://research.nhgri.nih.gov/homeodomain
Homeodomain sequences, structures and related genetic and genomic information
225. HORDE
http://bioinfo.weizmann.ac.il/HORDE/
Olfactory receptor genes and proteins
226. HUGE
http://www.kazusa.or.jp/huge/
Large (>50 kDa) human proteins and cDNA sequences
227. IMGT
http://imgt.cines.fr/
Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates
228. IMGT/HLA
http://www.ebi.ac.uk/imgt/hla/
Polymorphic sequences of human MHC and related genes
229. IMGT/MHC Database
http://www.ebi.ac.uk/imgt/mhc/
Major histocompatibility complex sequences
230. InBase
http://www.neb.com/neb/inteins.html
All known inteins (protein splicing elements): properties, sequences, bibliography
231. InterPro
http://www.ebi.ac.uk/interpro
Protein families and domains
232. Kabat Database
http://immuno.bme.nwu.edu/
Sequences of proteins of immunological interest
233. LGICdb
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
Ligand-gated ion channel subunit sequences
234. Lipase Engineering Database
http://www.led.uni-stuttgart.de/
Integrated information on sequence, structure and function of lipases and esterases
235. MEROPS
http://www.merops.ac.uk/
Proteolytic enzymes (proteases/peptidases)
236. MetaFam
http://metafam.ahc.umn.edu/
Integrated protein family information
237. Metalloprotein Database and Browser
http://metallo.scripps.edu/
Metal-binding sites in metalloproteins
238. MitoDrome
http://bighost.area.ba.cnr.it/BIG/MitoDrome
Drosophila nuclear genes encoding proteins targeted to the mitochondrion
239. MHCPEP
http://wehih.wehi.edu.au/mhcpep/
MHC-binding peptides
240. MPIMP
http://millar3.biochem.uwa.edu.au/~lister/index.html
Mitochondrial protein import machinery of plants
241. Nuclear Protein Database (NPD)
http://npd.hgu.mrc.ac.uk/
Proteins localized in the nucleus
242. Nuclear Receptor Resource
http://nrr.georgetown.edu/nrr/nrr.html
Nuclear receptor superfamily
243. NRMD
http://www.receptors.org/NR/
Nuclear receptor superfamily
244. NUREBASE
http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
Nuclear hormone receptors
245. Olfactory Receptor Database
http://ycmi.med.yale.edu/senselab/ordb/
Sequences for olfactory receptor-like molecules
246. ooTFD
http://www.ifti.org/
Transcription factors and gene expression
247. PANTHER
http://panther.celera.com/
Gene products organized by biological function
248. Peptaibol
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html
Peptaibol (antibiotic peptide) sequences
249. PhosphoBase
http://www.cbs.dtu.dk/databases/PhosphoBase/
Protein phosphorylation sites
250. PIR-NREF
http://pir.georgetown.edu/pirwww/pirnref.shtml
Non-redundant reference database with comprehensive protein sequences
251. PKR
http://pkr.sdsc.edu/
Protein kinase sequences, enzymology,genetics and molecular and structural properties
252. PLANT-PIs
http://bighost.area.ba.cnr.it/PLANT-PIs
Plant protease inhibitors
253. PlantsP/PlantsT
http://plantsp.sdsc.edu/
Functional geomics databases focusing on protein involved in plant phosphorylation and membrane transport, respectively
254. PPMdb data
http://sphinx.rug.ac.be:8080/ppmdb/index.html
Arabidopsis plasma membrane protein sequence and expression data
255. Prolysis
http://delphi.phys.univ-tours.fr/Prolysis/
Proteases and natural and synthetic protease inhibitors
256. Protein Information Resource (PIR)
http://pir.georgetown.edu/
Comprehensive, annotated, non-redundant protein sequence databases
257. ProtoNet
http://www.protonet.cs.huji.ac.il/
Hierarchical clustering of SWISS-PROT
258. Ribonuclease P Database
http://www.mbio.ncsu.edu/RNaseP/home.html
RNase P sequences, alignments and structures
259. RTKdb
http://pbil.univ-lyon1.fr/RTKdb/
Receptor tyrosine kinase sequences
260. S/MARt dB
http://transfac.gbf.de/SMARtDB/
Nuclear scaffold/matrix attached regions
261. SDAP
http://fermi.utmb.edu/SDAP
Sequences, structures and IgE epitopes of allergenic proteins
262. SENTRA
http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html
Sensory signal transduction proteins
263. SEVENS
http://sevens.cbrc.jp/
7-transmembrane helix receptors
264. SRPDB
http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
Structural and functional information on signal recognition particles
265. SWISS-PROT/TrEMBL
http://www.expasy.ch/sprot
Curated protein sequences
266. TIGRFAMs
http://www.tigr.org/TIGRFAMs
Functional identification of proteins
267. TRANSFAC
http://transfac.gbf.de/TRANSFAC/index.html
Transcription factors and binding sites
268. trEST, trGEN, Hits
http://hits.isb-sib.ch/
Hypothetical protein sequences
269. VIDA
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html
Homologous viral protein families
270. Wnt Database
http://www.stanford.edu/~rnusse/wntwindow.html
Wnt proteins and phenotypes
l Protein Sequence Motifs
271. ASC—Active Sequence Collection
http://crisceb.unina2.it/ASC/
Biologically-active short amino acid sequences
272. Blocks
http://blocks.fhcrc.org/
Multiple alignments of conserved regions of protein families
273. CDD
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Alignment models for conserved protein domains
274. CluSTr
http://www.ebi.ac.uk/clustr/
Automatic classification of SWISS-PROT+TrEMBL proteins
275. eMOTIF
http://motif.stanford.edu/emotif
Protein sequence motif determination and searches
276. InterPro domains
http://www.ebi.ac.uk/interpro/
Integrated documentation resource for protein families, domains, and sites
277. iProClass
http://pir.georgetown.edu/iproclass/
Annotated protein database with family,function and structure information
278. NESbase 1.0
http://www.cbs.dtu.dk/databases/NESbase
Nuclear export signals
279. NLSdb
http://cubic.bioc.columbia.edu/db/NLSdb/
Nuclear localization signals
280. GLYCBASE
http://www.cbs.dtu.dk/databases/OGLYCBASE/
O- and C-linked glycosylation sites in proteins
281. Pfam
http://www.sanger.ac.uk/Software/Pfam/
Multiple sequence alignments and hidden Markov models of common protein domains
282. PIR-ALN
http://pir.georgetown.edu/pirwww/dbinfo/piraln.html
Protein sequence alignments
283. PRINTS
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
Hierarchical gene family fingerprints
284. ProClass patterns
http://pir.georgetown.edu/gfserver/proclass.html
Protein families defined by PIR superfamilies and PROSITE patterns
285. ProDom
http://www.toulouse.inra.fr/prodom.html
Protein domain families
286. PROSITE
http://www.expasy.org/prosite
Biologically-significant protein patterns and profiles
287. ProtoMap
http://protomap.cornell.edu/
Automated hierarchical classification of SWISS-PROT proteins
288. SBASE
http://www.icgeb.org/sbase
Protein domain sequences and tools
289. SMART
http://smart.embl-heidelberg.de/
Simple Modular Architecture Research Tool
290. SUPFAM
http://pauling.mbu.iisc.ernet.in/~supfam
Grouping of sequence familieinto superfamilies
291. SYSTERS, GeneNest, SpliceNest
http://cmb.molgen.mpg.de/
Integrated database of protein families, EST clusters and their genomic positions
292. TMPDB
http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
Experimentally-characterized transmembrane topologies
l Proteome Resources
293. AAindex
http://www.genome.ad.jp/aaindex/
Physicochemical and biological properties of amino acids
294. GELBANK
http://gelbank.anl.gov/
2D-gel electrophoresis patterns from completed genomes
295. PEP: Predictions for Entire Proteomes
http://cubic.bioc.columbia.edu/pep/
Summarized analyses of protein sequences
296. Proteome Analysis Database
http://www.ebi.ac.uk/proteome/
Online application of InterPro and cluSTr for the functional classification of proteins in whole genomes
297. REBASE
http://rebase.neb.com/rebase/rebase.html
Restriction enzymes and associated methylases
298. SWISS-2DPAGE
http://www.expasy.org/ch2d/
Annotated two-dimensional polyacrylamide gel electrophoresis Database
l Retrieval Systems and Database Structure
299. TESS
http://www.cbil.upenn.edu/tess
Transcription element search system
300. Virgil
http://www.infobiogen.fr/services/virgil
Database interconnectivity
l RNA Sequences
301. 16S and 23S Ribosomal RNA Mutation Database
http://www.fandm.edu/Departments/Biology/Databases/RNA.html
16S and 23S ribosomal RNA mutations
302. 5S Ribosomal RNA Database
http://biobases.ibch.poznan.pl/5SData/
5S rRNA sequences
303. ACTIVITY
http://util.bionet.nsc.ru/databases/activity.html
Functional DNA/RNA site activity
304. ARED
http://rc.kfshrc.edu.sa/ared
AU-rich element-containing mRNAs
305. Database for mobile group II introns
http://www.fp.ucalgary.ca/group2introns/
Database for mobile group II introns
306. Guide RNA Database
http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
Guide RNA sequences
307. HyPaLib
http://bibiserv.techfak.uni-bielefeld.de/HyPa/
Structural elements characteristic for classes of RNA
308. Intronerator
http://www.cse.ucsc.edu/~kent/intronerator/
RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences
309. IRESdb
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
Internal ribosome entry sites
310. NCIR
http://prion.bchs.uh.edu/bp_type/
Non-standard base-base interactions in known RNA structures
311. Noncoding regulatory RNAs database
http://biobases.ibch.poznan.pl/ncRNA/
Noncoding RNAs with regulatory functions
312. PLANTncRNAs
http://www.prl.msu.edu/PLANTncRNAs/
Plant non-protein coding RNAs with relevant gene expression information
313. Plant snoRNA DB
http://www.scri.sari.ac.uk/plant_snoRNA/
snoRNA genes in plant species
314. PLMItRNA
http://bighost.area.ba.cnr.it/PLMItRNA/
Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
315. PseudoBase
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
Structural, functional and sequence data related to RNA pseudoknots
316. Rfam
http://www.sanger.ac.uk/Software/Rfam/
Non-coding RNA families
317. Ribosomal Database Project (RDP-II)
http://rdp.cme.msu.edu/
rRNA sequence data, analysis tools, alignments and phylogenies
318. RISCC
http://ulises.umh.es/RISSC
Ribosomal 16S–23S RNA gene spacer regions
319. RNA Modification Database
http://medlib.med.utah.edu/RNAmods/
Naturally modified nucleosides in RNA
320. SELEXdb
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
Selected DNA/RNA functional site sequences
321. Small RNA Database
http://mbcr.bcm.tmc.edu/smallRNA
Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
322. SRPDB
http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
Signal recognition particle RNA, SRP protein and SRP receptor sequences and alignments
323. Subviral RNA Database
http://penelope.med.usherb.ca/subviral/
Database of viroids and viroid-like RNAs
324. tmRDB
http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
tmRNA (10Sa RNA) sequences and alignments
325. tRNA Sequences
http://www.uni-bayreuth.de/departments/biochemie/trna/
tRNA and tRNA gene sequences
326. tmRNAWebsite
http://www.indiana.edu/~tmrna
tmRNA sequences, foldings, and alignments
327. UTRdb/UTRsite
http://bighost.area.ba.cnr.it/srs6/
5- and 3-UTRs of eukaryotic mRNAs and relevant functional patterns
328. Yeast snoRNA Database
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
Yeast small nucleolar RNAs
l Structure
329. ASTRAL
http://astral.stanford.edu/
Sequences of domains of known structure, selected subsets and sequence-structure correspondences
330. BioMagResBank acids
http://www.bmrb.wisc.edu/
NMR spectroscopic data from proteins peptides, and nucleic acids
331. CADB
http://144.16.71.148/
Conformation angles of protein structures, with associated crystallographic data
332. CATH
http://www.biochem.ucl.ac.uk/bsm/cath_new
Protein domain structures
333. CE
http://cl.sdsc.edu/ce.html
CE: a resource to compute and review 3D protein structure alignments
334. CKAAPs DB
http://ckaap.sdsc.edu/
Structurally-similar proteins with dissimilar sequences
335. CSD
http://www.ccdc.cam.ac.uk/prods/csd/csd.html
Crystal structure information for organic and metal organic compounds
336. Database of Macromolecular Movements
http://bioinfo.mbb.yale.edu/MolMovDB/
Descriptions of protein and macromolecular motions, including movies
337. Decoys ‘R’ Us
http://dd.stanford.edu/
Computer-generated protein conformations based on sequence data
338. DSDBASE
http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
Native and modeled disulfide bonds in proteins
339. DSMM
http://projects.eml.org/mcm/database/dsmm
Database of Simulated Molecular Motions
340. E-MSD
http://www.ebi.ac.uk/msd
Collected data on macromolecular structures
341. FAMSBASE
http://famsbase.bio.nagoya-u.ac.jp/famsbase/
Protein three-dimensional structural models
342. Gene3D
http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
Precalculated structural assignments for genes within whole genomes
343. GTOP
http://spock.genes.nig.ac.jp/~genome/gtop.html
Protein fold predictions from genome sequences
344. HIC-Up
http://alpha2.bmc.uu.se/hicup/
Structures of small molecules (‘hetero-compounds’)
345. HSSP
http://www.sander.ebi.ac.uk/hssp/
Structural families and alignments; structurarlly-conserved regions and domain architecture
346. IMB Jena Image Library of Biological Macromolecules
http://www.imb-jena.de/IMAGE.html
Visualization and analysis of three-dimensional biopolymer structures
347. ISSD
http://www.protein.bio.msu.su/issd/
Integrated sequence and structural information
348. LPFC
http://www-smi.stanford.edu/projects/helix/LPFC/
Library of protein family core structures
349. MMDB linked
http://www.ncbi.nlm.nih.gov/Structure/
All experimentally-determined three-dimensional structures, linked to NCBI Entrez
350. MolMovDB
http://molmovdb.org/
Database of macromolecular movements
351. ModBase
http://guitar.rockefeller.edu/modbase
Annotated comparative protein structure models
352. NDB
http://ndbserver.rutgers.edu/
Nucleic acid-containing structures
353. NTDB
http://ntdb.chem.cuhk.edu.hk/
Thermodynamic data for nucleic acids
354. PALI
http://pauling.mbu.iisc.ernet.in/~pali
Phylogeny and alignment of homologous protein structures
355. PASS2
http://ncbs.res.in/~faculty/mini/campass/pass.html
Structural motifs of protein superfamilies
356. PDB
http://www.pdb.org/
Structure data determined by X-raycryst allography and NMR
357. PDB-REPRDB
http://www.cbrc.jp/pdbreprdb/
Representative protein chains, based on PDB entries
358. PDBsum
http://www.biochem.ucl.ac.uk/bsm/pdbsum
Summaries and analyses of PDB structures
359. PRESAGE
http://presage.berkeley.edu/
Protein structures with experimental and predictive annotations
360. ProTherm
http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html
Thermodynamic data for wild-type and mutant proteins
361. PSSH
http://srs3d.ebi.ac.uk/
Alignments between protein sequences and tertiary structures
362. RESID
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html
Protein structure modifications
363. RNABase
http://www.rnabase.org/
RNA-containing structures from PDB and NDB
364. SCOP
http://scop.mrc-lmb.cam.ac.uk/scop
Familial and structural protein relationships
365. SCOR
http://scor.lbl.gov/
RNA structural relationships
366. Sloop
http://www-cryst.bioc.cam.ac.uk/~sloop/
Classification of protein loops
367. Structure-Superposition Database
http://ssd.rbvi.ucsf.edu/
Pairwise superposition of TIM-barrel structures
368. SUPERFAMILY
http://supfam.org/
Assignments of proteins to structural superfamilies
l Transgenics
369. Cre Transgenic Database
http://www.mshri.on.ca/nagy/cre.htm
Cre transgenic mouse lines
370. Transgenic/Targeted Mutation Database
http://tbase.jax.org/
Information on transgenic animals and targeted mutations
l Varied Biomedical Content
371. BAliBASE alignments
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
Benchmark database for comparison of multiple sequence alignments
372. Cytokine Gene Polymorphism in Human Disease
http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm
Cytokine gene polymorphism literature database
373. DBcat
http://www.infobiogen.fr/services/dbcat/
Catalog of databases
374. Global Image Database
http://www.gwer.ch/qv/gid/gid.htm
Annotated biological images
375. GlycoSuiteDB
http://www.glycosuite.com/
N- and O-linked glycan structures and biological source information
376. Imprinted Genes and Parent-of-Origin Effects
http://www.otago.ac.nz/IGC
Imprinted genes and parent-of-origin effects in animals
377. MPDB
http://www.biotech.ist.unige.it/interlab/mpdb.html
Information on synthetic oligonucleotides proven useful as primers or probes
378. NCBI Taxonomy Browser
http://www.ncbi.nlm.nih.gov/Taxonomy/
Names of all organisms that are represented in the genetic databases with at least one nucleotide orprotein sequence
379. probeBase
http://www.probebase.net/
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information
380. PubMed
http://www.ncbi.nlm.nih.gov/PubMed/
MEDLINE and Pre-MEDLINE citations
381. RefSeq
http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html
Reference sequence standards for genomes, genes, transcripts and proteins
382. RIDOM
http://www.ridom.de/
rRNA (16S and ITS) sequence-based identification of medical microorganisms
383. SWEET-DB
http://www.dkfz-heidelberg.de/spec2/sweetdb/
Annotated carbohydrate structure and substance information
The Pharmacogenomics and Pharmacogenetics
384. Knowledge Base
http://www.pharmgkb.org/
Variation in drug response based on human variation
385. Tree of Life
http://phylogeny.arizona.edu/tree/phylogeny.html
Information on phylogeny and biodiversity
386. Vectordb
http://www.atcg.com/vectordb/
Characterization and classification of nucleic acid vectors
387. VirOligo
http://viroligo.okstate.edu/
Virus-specific oligonucleotides for PCR and hybridization
