[Bioperl-l] Question about the definition of 'gaps' in blast -m8 output...

Dave Messina David.Messina at sbc.su.se
Fri Mar 20 14:14:00 EDT 2009

Hey Dan,

> where can I read more about selecting parameters for certain tasks?

I like the Korf, Yandell, and Bedell BLAST
book<http://www.amazon.com/Blast-Ian-Korf/dp/0596002998>from O'Reilly.

For your tomato/potato, I would look at some of the specialized genomic
aligners, for example LAGAN<http://lagan.stanford.edu/lagan_web/index.shtml>
 or AVID <http://baboon.math.berkeley.edu/mavid/>.


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