【转帖】DNA或者PROTEIN序列分析的总思路
丁香园论坛
1242
DNA或者PROTEIN序列分析的总思路，含网上软件
希望对大家有帮助！
此主题相关图片如下：
Program Function
Blastn Nucleotide query against nucleotide database
Blastp Protein query against protein database
Blastx Nucleotide query against protein database
Pairwise blast Comparison of two nucleotide or protein seqs
CD search Conserved domain search
Domain search:
l Most genes/proteins in the database do not have an assigned function. Such sequences show “no hits” or have similarity to conserved hypothetical proteins in the BLAST search results.
l One way to assign a tentative function to an unknown protein is to search for conserved domains in that protein because domains are usually the functional units in proteins.
l Strategy: similar to BLAST, local alignment analysis. Hidden Markov Model is used.
Signal peptide prediction
l Secreted and/or transmembrane proteins are likely to be important in antigenic profile and contact with host cells because they are surface exposed.
l In general, secreted and transmembrane proteins have signal peptide at the N-terminus.
l Signal peptide has a common structure of a positively charged n-region followed by a hydrophobic h-region and a neutral but polar c-region.
l Also, there is a (-3,-1) rule which is saying that residues at positions of –3 and –1 (relative to the cleavage site) must be small and neutral.
Signal output parsing
l NN predictin score (neural network value)
l HMM prediction score
l Cleavage sites prediction by NN and HMM.
l Criteria for a protein likely has signal peptide: NN and HMM scores are greater that 0.8; and cleavage sites predicted by both are the same.
Useful bio-home links:
l ORF-finder at NCBI: http://www.ncbi.nlm.nih.gov/gorf/gorf.html
l GETORG: http://bioweb.pasteur.fr/seqanal/interfaces/getorf.html
l BLAST: http://www.ncbi.nlm.nih.gov/BLAST/
l Protein domain: Pfam: http://pfam.wustl.edu/hmmsearch.shtml
l SignalP2.0: http://www.cbs.dtu.dk/services/SignalP-2.0/#submission
l SignalP3.0: http://www.cbs.dtu.dk/services/SignalP/
l TRNAscan-SE: http://www.genetics.wustl.edu/eddy/tRNAscan-SE
l Biotools: http://www.up.univ-mrs.fr/~wabim/english/logligne.html
(感谢mybbff 的提醒)
希望对大家有帮助！
此主题相关图片如下：
Program Function
Blastn Nucleotide query against nucleotide database
Blastp Protein query against protein database
Blastx Nucleotide query against protein database
Pairwise blast Comparison of two nucleotide or protein seqs
CD search Conserved domain search
Domain search:
l Most genes/proteins in the database do not have an assigned function. Such sequences show “no hits” or have similarity to conserved hypothetical proteins in the BLAST search results.
l One way to assign a tentative function to an unknown protein is to search for conserved domains in that protein because domains are usually the functional units in proteins.
l Strategy: similar to BLAST, local alignment analysis. Hidden Markov Model is used.
Signal peptide prediction
l Secreted and/or transmembrane proteins are likely to be important in antigenic profile and contact with host cells because they are surface exposed.
l In general, secreted and transmembrane proteins have signal peptide at the N-terminus.
l Signal peptide has a common structure of a positively charged n-region followed by a hydrophobic h-region and a neutral but polar c-region.
l Also, there is a (-3,-1) rule which is saying that residues at positions of –3 and –1 (relative to the cleavage site) must be small and neutral.
Signal output parsing
l NN predictin score (neural network value)
l HMM prediction score
l Cleavage sites prediction by NN and HMM.
l Criteria for a protein likely has signal peptide: NN and HMM scores are greater that 0.8; and cleavage sites predicted by both are the same.
Useful bio-home links:
l ORF-finder at NCBI: http://www.ncbi.nlm.nih.gov/gorf/gorf.html
l GETORG: http://bioweb.pasteur.fr/seqanal/interfaces/getorf.html
l BLAST: http://www.ncbi.nlm.nih.gov/BLAST/
l Protein domain: Pfam: http://pfam.wustl.edu/hmmsearch.shtml
l SignalP2.0: http://www.cbs.dtu.dk/services/SignalP-2.0/#submission
l SignalP3.0: http://www.cbs.dtu.dk/services/SignalP/
l TRNAscan-SE: http://www.genetics.wustl.edu/eddy/tRNAscan-SE
l Biotools: http://www.up.univ-mrs.fr/~wabim/english/logligne.html
(感谢mybbff 的提醒)
