[Bioperl-l] Finding Alignment overlaps

[zayed albertyn]

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




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Zayed Albertyn