[Bioperl-l] Finding Alignment overlaps

[Jason Stajich]

Bio::SeqFeature::Collection lets you efficiently extract subsets of 
Features or Locations that overlap using Lincoln's binning algorithm 
that is in Bio::DB::GFF.  It is done storing data in a flatfile 
BerkeleyDB  B-Trees using the DB_File module.

-jason
On Jan 14, 2005, at 1:50 AM, zayed albertyn wrote:

> Dear Bioperl Community
>
> I have output from an alignment program that produces coordinates with
> reference to the query sequence e.g.
>
> 3665384,3665702-1770163,1770480
> 3665130,3665474-3695657,3696000
> 3665115,3665357-1770508,1770749
>
> Each line represent <querybegin>,<queryend>-<targetbegin>,<targetend>
>
> I know how to add each line as a sequence feature using
> Bio::Seqfeature::Generic. Is there a bioperl class or associated
> method that can be used for determing possible overlaps in these
> alignments?
> Eventually I would like to find all overlaps and merge them if 
> possible.
>
> Thanks for the help,
> Zayed
>
>
>
>
> -- 
> -----------------------------------------------------------
> Zayed Albertyn
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>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/