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

Dan Bolser dan.bolser at gmail.com
Wed Mar 18 18:30:16 EDT 2009

2009/3/18 Phillip San Miguel <pmiguel at purdue.edu>

> 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.

Yeah, I'll have to go look at the HSPs to confirm this... I'm just surprised
that there are not more gaps of length >1. i.e. my data (given your
interpretation) suggests that 90% of the HSPs have no gaps > length 1.

However, it would make sense given the roughly linear relationship between
the discrepancy and the total number of gaps. I'll let you know.



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