[Bioperl-l] Fwd: blast result not matching.

Dave Messina David.Messina at sbc.su.se
Fri Sep 9 05:40:25 EDT 2011

Hi Manju,

But this is not showing all query coverage as it shows in simple balst.(see
> attached file)

I'm not sure what you mean by query coverage here, as blast report you
attached doesn't (as far as I can see) include a calculation of the number
or percentage of query bases covered.

But in any case, everything in that blast report is available in the
Bio::SearchIO object that B::T::R::RemoteBlast returns. Have you taken a
look at http://www.bioperl.org/wiki/HOWTO:SearchIO ? That, along with the
module documentation, should help you find the parts of the BLAST report
you're looking for.

> and i also want to write that result in a blast file..Is there any method
> which can write the remoteblast output
> in a file with blast extension?

It is possible to write out the results in a format that closely resembles
the native blast report, but it's not recommended. If you want to just run
BLAST and get back a report, there's no need to use BioPerl to parse the
report first and then recreate the report.

This might also be a good time to mention that, if you're doing more than a
few hundred BLAST searches, you'll find it much more efficient to download
the database and the BLAST program from NCBI and run them on your own
computer. NCBI severely limits the speed and frequency of remote BLASTs, and
furthermore it's much more prone to failure.

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
remotely without BioPerl. Check out the --remote command-line option — it's
my favorite new feature!


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