[Bio-Linux] Blasting Multiple Fasta Files

[Zain A Alvi]

Hi Marty,

I apologize for the confusion. I am splitting a fasta file that contains approximately 100,000 fasta sequences to 100 fasta files that contains 1000 sequences each.  I am hoping this will expedite the BLASTx process.


Kind regards,


Zain

________________________________
From: Martin Gollery <mgollery at unr.edu>
Sent: Tuesday, May 5, 2015 10:23 AM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Blasting Multiple Fasta Files

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<mailto: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
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