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Old 11-27-2015, 03:02 PM   #1
Location: US

Join Date: Feb 2011
Posts: 24
Default search homopolymers


I'd like to look for homopolymers in a genome. Is there any program can find it easily?

I wrote a script and simply found out all the patterns like "AAAA...", "CCC...", length from 2 to 10. But I am afraid those outputs may not be true. Somebody told me Novoalign can work on this but it is not free.

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Old 11-27-2015, 07:10 PM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

If you have more confidence in someone else's code than your own, you could use the EMBOSS program dreg.
Several published papers have used it to identify homopolymers.

One among several papers that used dreg to identify homopolymers:
"Homopolymeric tracts represent a general regulatory mechanism in prokaryotes"

Last edited by blancha; 11-27-2015 at 07:49 PM.
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Old 11-27-2015, 11:29 PM   #3
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 836

I use a Perl regular expression to find homopolymers in my fasta2svg code:

$tSeq = $base_sequence;
$hl = $homopolymer_minimum_length;
while($tSeq =~ s/^(.*?)(A{$hl,}|C{$hl,}|G{$hl,}|T{$hl,})//){
  printf("Non-homopolymer sequence: $1\n");
  printf("Homopolymer sequence: $2\n");
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Old 12-02-2015, 06:23 PM   #4
Location: US

Join Date: Feb 2011
Posts: 24

Thank you very much! I will try drug and gringer's code. Thanks!
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