[Bioperl-l] BL2SEQ

Barry Moore barry.moore at genetics.utah.edu
Thu Mar 31 15:04:05 EST 2005

I agree with Sean.  Installing BLAST locally is really quite easy on 
most platforms (Unix and Window from my experience).  Download the 
binaries from here ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST, 
and get documentation here http://www.ncbi.nlm.nih.gov/BLAST/docs/.  You 
would unpack and install the binaries, run formatdb on a fasta file of 
all your sequences, and then use bioperl to loop over all of your 
sequences and blast each one against the database.  See the module 
documentation for StandAloneBlast here to see how to actually run local 
BLAST with bioperl.  Using bioperl can also help alot with parsing all 
the resulting blast output.  Read some of the HOWTO's at 
http://www.bioperl.org/Core/Latest/modules.html.  Specifically, have a 
look at the SearchIO HOWTO, and if you're new to bioperl have a look at 
Beginners HOWTO and SeqIO HOWTO for starters.  If you really want to 
move forward with remote BLAST see this modules documentation 
However, if you have alot of sequences, this will become very slow.  You 
won't like it, and neither will NCBI.


Sean Davis wrote:

> 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
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Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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