[Bioperl-l] SearchIO

[Jason Stajich]

Make sure you read the SearchIO HOWTO there is a table outlining
all of the data that is accessible in the Search objects.

Some lengths:
query sequence length:
 $result->query_length
hit sequence length
 $hit->length

HSP length (gaps in both query and hit)
 $hsp->hsp_length OR $hsp->length('total')

Query HSP length (participating in the alignment, ungapped abs(start - end))
 $hsp->query->length OR $hsp->length('query')

Hit HSP length (participating in the alignment, ungapped abs(start - end))
 $hsp->hit->length or $hsp->length('hit')


--jason
On Fri, 30 Jan 2004, [iso-8859-1] william ritchie wrote:

> Hi,
> I would like to know if there is a way to retrieve a
> blast SUBJECT length, not the hit length or the query
> length!!
> Thanks.
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu