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|
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;
l CD search: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi;
l Structure search: http://www.ncbi.nlm.nih.gov/Structure/;
l Pairwise blast: http://www.ncbi.nlm.nih.gov/BLAST/bl2seq/bl2.html
