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

[Phillip San Miguel]

Dan Bolser wrote:
> 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.
>   
Sounds about right. Depends on how you have gap opening vs gap 
lengthening parameters set.

-- 
Phillip