This may help. Not polished or thoroughly tested, but should get you to a starting point.

enjoy!
dageek

#!/usr/bin/perl -w
use strict;
## set minimum length for polytail to search for
my $polytail_min_len = 10;
my $polytail_curr_len = $polytail_min_len;
my $workline;
my $polya_str_base;
## read data record
for (<DATA>)
{
## remove exteranious characters
  s/[\r\n]//g;
# add new data to end of working data string
  $workline = $workline . $_;
  while (length($workline) > $polytail_curr_len)
  {
      $polya_str_base = substr($workline,0,$polytail_curr_len);
## remove desired characters from string
      $polya_str_base =~ s/[AN]//g;
## no characters left = all characters were in desired character set
      if (length($polya_str_base) == 0)
      {
## add a character from data set to string to test (ok - bump subscrip
+t)
        $polytail_curr_len++;
      }
      else
      {
## a polytail of at least minimum length was found
         if ($polytail_curr_len > $polytail_min_len)
         {
           print substr($workline,0,$polytail_curr_len-1) . "\n";
## trim characters of found polytail from working string
           $workline = substr($workline,$polytail_curr_len);
## reset length of string to test
           $polytail_curr_len = $polytail_min_len;
         }
## trim lead character from working field
         $workline = substr($workline,1);
      }
  }
}

__DATA__
123456789abcdefghijklmnopqrstuvwxyz
ACGGAAAAAAAAAAATCGGATCTGAATGTCTAGAGGGGTTCTCTCCCTTGGTGTGAGTCTAGCCCTGAAA
+GTTGCANANAN
NANANAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAA
NTCCCACTCTANCGCGAAGCCAAATTTGTCGAGAGTACTCTGGGGGGAAGAGATCAGAATTGTGCAGACT
+AATCCGTAACTGC
CAAGTACTATTGGCCCTGTTCCAACCATCTAACCTCCTTATGATAACCATGCCACTAAATGGGTTCCTGG
+ATCTGCACCT
CATTCGCTCGCCTTATGGCCTCGGCTCTCTGCGTATCCACCCTCCTCGTCACCGCCATGCCCTTCGACCT
+TCAGCGGGGG

[download]

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

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