[Bioperl-l] BL2SEQ

[Sean Davis]

On Mar 31, 2005, at 10:15 AM, Mane, Ajay ((UMR-Student)) wrote:

> Thanks for the reply.
>
> I have lots of sequence pairs which i want to align. Two sequences at 
> a time. I want to form some statistics on the alignment results. That 
> is about the coding regions in nucleotides. I need to manually look at 
> the coding regions everytime and do some analysis. Instead, i want to 
> run a perl file which runs the bl2seq on blast server, gets the 
> results, formats them to provide some statistics which i am interested 
> in. I do not want to install blast locally on my machine. I just have 
> lots of accession numbers in a file and want to display statistics of 
> all of them in some file/files using a perl file. I have succeeded to 
> a limit using the normal perl, by submitting accession numbers and 
> getting results from blast server using http::request methods. But i 
> want to know how to use Bioperl for this job.
>

I know you said you do not want to install blast on your machine, but 
if you have many accessions and want to blast all pairs, using local 
blast would be very convenient--just blast all sequences against all 
other sequences.  There are binaries for many platforms, so you 
probably wouldn't even have to build the blast executables.

Sean