# report.rb

Path: | lib/bio/appl/blat/report.rb
Last Update: | Tue Feb 01 03:26:53 +0000 2011

# bio/appl/blat/report.rb - BLAT result parser

Copyright: | Copyright (C) 2004, 2006, 2008 Naohisa Goto <ng@bioruby.org>
License: | The Ruby License

     $Id:$

BLAT result parser (psl / pslx format).

## Important Notes

In BLAT results, the start position of a sequnece is numbered as 0. On the other hand, in many other homology search programs, the start position of a sequence is numbered as 1. To keep compatibility, the BLAT parser adds 1 to every position number.

## References

- Kent, W.J., BLAT—the BLAST-like alignment tool, Genome Research, 12, 656—664, 2002. www.genome.org/cgi/content/abstract/12/4/656
- genome.ucsc.edu/goldenPath/help/blatSpec.html

### Required files

bio

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