[Bioperl-l] coordinate issue with Bio::SearchIO::psl

Elliott H Margulies elliott at nhgri.nih.gov
Tue Mar 23 13:36:32 EST 2004

Dear BioPerl Developers:

I have been evaluating the use of BioPerl for parsing BLASTZ lav
output. To do this, I convert the lav output to 'psl' format with Jim
Kent's lavToPsl program.

When I report some stats about the alignments from within BioPerl, I
notice that lengths and stop positions are 1 *greater* than they should

I'm pretty sure this is a reflection of the fact that psl output is in
the infamous half-open zero-based coordinate system and not simply
zero-based closed intervals.

Please let me know how I can help facilitate this fix, if it is in fact
confirmed to be true.


Elliott H. Margulies, Ph.D.
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
50 South Dr., MSC 8004
Bldg. 50, Rm. 5527
Bethesda, MD  20892-8004

phone: (301) 594-9210
fax: (301) 496-0474

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