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Re: BioInformatics - polyA tail search

by biosysadmin (Deacon)
on Sep 03, 2003 at 10:00 UTC ( #288573=note: print w/replies, xml ) Need Help??

in reply to BioInformatics - polyA tail search

Dear Perlmonks, I have not yet had time to delve into BioPerl (although I can't wait!).

Here's a brief introduction to Bioperl for you:
#!/usr/bin/perl -w use strict; use Bio::SeqIO; my @files = <*.seq>; my $pattern = '[AN]{10}'; foreach my $file (@files) { my $seqio = Bio::SeqIO->new( -file => $file ); while ( my $seqobj = $seqio->next_seq() ) { my $raw_seq = $seqobj->seq(); if ( $raw_seq =~ /$pattern/o ) { print "Found a polyA tail in $file.\n"; } } }
This seems to work for me.

If you have any questions about how it works, just ask. I made a few assumptions:
  • If there were a sequence file with 4 sequences, two of which had poly-A tails, the program would print:
    Found a polyA tail in myfile Found a polyA tail in myfile
  • I'm assuming that you're using some sort of format that Bioperl supports.
Also, is there community interest in an Intro to Bioperl Tutorial? The documentation at seems to be very geared towards developers and other experienced Bioperl users. If there is interest I'd be happy to write it, alhough I might need some help (I'm a long time reader of PM, short time member).

Replies are listed 'Best First'.
Re: Re: BioInformatics - polyA tail search
by Anonymous Monk on Sep 03, 2003 at 12:14 UTC
    There *is* a BioPerl tutorial, along with a huge variety of sample scripts in the BioPerl distribution. I think additional BioPerl tutorial material is a great idea, but don't put it here: contribute it back to the main project. The core developers there are too overloaded to do this kind of stuff, I think.

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