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