Finding Genes in Genomic Nucleotide Sequences by Using Bioinformatics

互联网2014-02-13

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You have, we hope, come to this chapter wishing to know how to use bioinformatics to locate genes in genomic sequences. You probably want to know which are the easiest and best tools to use, to treat them largely as black boxes, and to know how to assess the likely accuracy of the results you obtain. If so, you have come to the right place. In the absence of knowing which genome(s) you are interested in, we have chosen to take our examples from a variety of human, plant, pathogenic bacterial, and fungal genomes (see Table 1 ). Because access to computational resources varies greatly, we have chosen to restrict ourselves to describing methods that make use of computational resources (software and databases) that are publicly available on the Internet via the World Wide Web (see Table 2 ). We assume that you have access to the Internet, and that you know how to use a graphical Web browser such as Netscape Navigator or Microsoft Internet Explorer. We also assume that this is not your first acquaintance with using bioinformatics tools. Before attempting to work through this chapter, you should have run BLAST and be familiar with techniques for retrieving gene or protein sequences from data banks such as Swissprot or EMBL.

Table 1 Genomic DNA Fragments Used to Demonstrate Gene Prediction Methods by Using Bioinformatics

Organism	Division	Description	EMBL entry name	Accession no.	Sequence length (bp)
Homo sapiens	Human	Interleukin-2 receptor γ-chain	HSIL2RGA	L19546	4038
Mycobacterium Tuberculosis	Prokaryote	Erdman sigma factor rpoV	MT21134	U21134	2745
Oryza sativa	Plant	Receptor kinase-like protein (Xa21)	OS37133	U37133	3921
Saccaromyces pombe^a	Fungi	Data not sub-mitted to EMBL at time of writing	Not applicable	Not applicable	4250

^a The last fragment (c1592) was obtained from the S. pombe sequencing project based at the Sanger Center (http://www.sanger.ac.uk/Projects/S_pombe ). Fragment c1592 is from chromosome III.

Table 2 List of URLs for Tools Used to Predict Protein-Coding Regions in Genomic Sequences

Name	Home page URL for gene prediction programs	Refs.
BCM Gene Finder	http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html http://genomic.sanger.ac.uk/gf/gf.shtml	1
WebGeneMarkHmm	http://dixie.biology.gatech.edu/GeneMark/eukhmm.cgi	*2,3*
WebGeneMark	http://dixie.biology.gatech.edu/GeneMark/hmmchoice.html
GeneID3	http://www1.lmmes/software/geneid/geneid.html	4
Genie	http://www.fruitfly.org/seq_tools/genie.html	5
Genscan	http://bioweb.pasteur.fr/seqanal/interfaces/genscan.html	6
Grail	http://compbio.ornl.gov/Grail-1.3	*7,8*
HMMgene	http://www.cbs.dtu.dk/services/HMMgene/	9
BLASTX 2.0.10	http://www.ncbi.nim.nih.gov/BLAST	10

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