[Bioperl-l] finding position of every instance of a pattern in asequence

Marc Logghe Marc.Logghe at DEVGEN.com
Sat Sep 3 16:19:24 EDT 2005

Hi Andrew,
One way you could do it, is to use the external EMBOSS application
fuzznuc or dreg. There is a API available in bioperl-run
(Bio::Factory::EMBOSS). Nice thing is that you can give the EMBOSS
option -rformat2 gff so that your output is in GFF. The latter can
easily be turned into a feature object:
my $tag = Bio::SeqFeature::Generic->new(-gff_string => $gff); 


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> Andrew Stewart
> Sent: Friday, September 02, 2005 10:06 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] finding position of every instance of a 
> pattern in asequence
> I have problem I am trying to solve.  I know I can no doubt 
> rig up some regular perl code to solve it, but I'm wondering 
> if there is some BioPerl module that might make the task much simpler.
> I have a single sequence composed of a concatenation of 
> several contigs, with special 'contig boundary tags' marking 
> the transition between every of neighboring contigs. 
> I wrote a script that reads in the sequence, as well as 
> glimmer output from the sequence in order to create a series 
> of features (for output into a genbank file).  Because any of 
> these features spanning across these contig boundaries 
> probably isn't real, I also want to create a miscellaneous 
> feature whereever there is a 'contig boundary tag'.
> Basically what I need is a function that will search the 
> entire sequence for my tag sequence, and return a list of the 
> locations for every instance of it found in the sequence. 
> Can anyone direct me to a module that handles this sort of 
> thing, or do I need to rig it up outside of bioperl?
> Thanks,
> -Andrew Stewart
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