[Bioperl-l] Identifying bla(s)t hits which overlap

[Charles Hauser]

I'm interested in identifying assembled EST contigs which span genomic
scaffolds as a means of tying scaffolds together.  So, I would like to
find blast or blat hits which overlap:

schematic of bla(s)t hits:

        contig 1.xxx    ---------------------------------------------  
        scaffold 1         ----------------[--
        scaffold N                            --]-----------


It appears I need to use Bio::SimpleAlign but thought I'd ask if there
are other approaches?

Charles