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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 doc.bioperl.org 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).

In reply to Re: BioInformatics - polyA tail search by biosysadmin
in thread BioInformatics - polyA tail search by MiamiGenome

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