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

Phillip San Miguel pmiguel at purdue.edu
Wed Mar 18 16:12:19 EDT 2009

Dan Bolser wrote:
> Can someone clarify the definition of the 'gaps' column in the blast -m8
> output format for me?
> I thought that the column 'gaps' was basically the number of columns in the
> HSP that contains a gap character. 
Hi Dan,
"gaps", to me, denotes the number of gaps. Not the total length of all 
the gaps.
Just my interpretation, but given your results my guess is that whomever 
wrote blastall was thinking the way I do.

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