I want to use perl to find transcription factor DNA binding sites. For instance CACTTGAN. I only have basic perl writing comprehension but can follow a script fairly well. Thanks. ABC

This would be a rather crude way to search for TFBS's. There are many 'scanner' tools available that use PWWMs or PSSMs to find putative sites (and score them). I have used TRANSFAC's "match" tool as well as "patser" with some success. If you can get ahold of a PSSM for your transcription factor I would suggest scanners rather than strict regexes. Failing that, you could probably do what you need in a few lines of perl. Try what I have put below (keep in mind I haven't tested it).

#input is a fasta file of upstream sequences, you can get 1kb and 5kb upstream sequences pre-extracted from the UCSC genome browser download page

#!/usr/bin/perl
use strict;
use Bio::SeqIO;

my $pattern = "CACTTGA[ACTG]";

my $io = Bio::SeqIO->new(-file=>"upstream_1kb.fa",-format=>'fasta');

while(my $seq_obj = $io->next_seq){
my $full_sequence = uc($seq_obj->seq);
if($full_sequence =~ /$pattern/ ){
#this sequence matches, do something with it
my $id = $seq_obj->display_id;
print "$id has match on (+) strand\n";
}
my $rc = $seq_obj->revcom;
my $rc_seq = uc($rc->seq);
if($rc_seq =~ /$pattern/ ){
#this sequence matches, do something with it
my $id = $seq_obj->display_id;
print "$id has match on (-) strand\n";
}
}

Ya..

Why do you want to use a script? Are you after TFBS that aren't in the databases already?

e.g. Transfac or Oreganno.

-SC

I'm not partial to Perl at all....there are easier ways I know. I am learning to find known TF binding sites first so I can proceed to design scripts to find unknown TF's. So ultimately I'd like to use perl to search both strands (forward and reverse comlement) to do this. Thanks.

ABC

Are you familiar with, the $& function, I was told this may help?

I'll be using my output to compare results obtained through Patser and MEME for example. Then seeing which program spit out sequences which actually are known to bind TF's. I will be using Gibbs etc for the novel sites, I tried to simply what it is I need (perl script) now. Thanks for the interest.