Search Domains In A Protein Fasta File.

Question

[Persianswallow74]

Hi i wanted to write a script in perl that can finds domains in a protein.i have domains protein sequences in two fasta file.i want to search all domains in a protein and i want order of domains. thank you for your help. james.

[Michael Schubert]

Hi! I'd suggest you read http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/python/rpsblast/ (and ignore the biopython part).. if you're stuck somewhere you're welcome to refine your question.

[Aleksandr Levchuk]

I have a fully working and tested procedure for extracting domains here. :) Welcome to Biostars.org!

[Persianswallow74]

thank you,actually i have two question at first: 1)how can i extract protein sequences one by one from a fasta file? 2)how can i find domain sequences with their name in one file? thank you.

Answer 1

[Niallhaslam]

For the first part of your question I would suggest the bioperl library. This will handle the parsing of sequences from your input file.

For finding domains there is a perl script available from SMART for the parsing of domains from a fasta sequence automagically.