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Old 11-27-2015, 03:02 PM   #1
doublealice
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Default search homopolymers

Hi

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.

Thanks!
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Old 11-27-2015, 07:10 PM   #2
blancha
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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.

http://emboss.sourceforge.net/apps/c...apps/dreg.html

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

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