[Bioperl-l] Finding Alignment overlaps

[Allen Day]

yeah, look in Bio::Range.  specifically:

Geometrical methods
       These methods do things to the geometry of ranges, and return triplets
       (start, end, strand) from which new ranges could be built.

       intersection

         Title    : intersection
         Usage    : ($start, $stop, $strand) = $r1->intersection($r2)
         Function : gives the range that is contained by both ranges
         Args     : a range to compare this one to
         Returns  : nothing if they do not overlap, or the range that they do overlap
         Inherited: Bio::RangeI::intersection


       union

         Title    : union
         Usage    : ($start, $stop, $strand) = $r1->union($r2);
                  : ($start, $stop, $strand) = Bio::Range->union(@ranges);
         Function : finds the minimal range that contains all of the ranges
         Args     : a range or list of ranges
         Returns  : the range containing all of the ranges
         Inherited: Bio::RangeI::union

-allen


On Fri, 14 Jan 2005, 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
> 
> 
> 
> 
>