[Bio-Linux] Blasting Multiple Fasta Files

[Martin Gollery]

Running a million BLASTX jobs on one sequence each is not going to save you
time. It is better to run one BLASTX job on a million sequences.

-Marty


On Tue, May 5, 2015 at 7:00 AM, Zain A Alvi <zain.alvi at student.shu.edu>
wrote:

>  Dear Sir or Madam,
>
>
>  I hope everything is well. I have downloaded all the viral protein
> sequences from the NCBI refseq database using their script from their
> E-book.  I have de-novo assembled some viral genomes and I know BLASTX
> takes a long time if the fasta is large.  I have been able to split the
> large fasta file based on an user specified contig number in each new fasta
> file.
>
>
>  I was wondering is there a method to run BLASTX automatically on each of
> the fasta files one at a time so that it will be able to complete in a
> "shorter" amount of time as compared to BLASTing the whole large de-novo
> assembled fasta file.  Then I was hoping to concatenate all the results
> into one file.
>
>
>  Sincerely,
>
>
>  Zain
>
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>


-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com
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