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<p>Hi Marty,<br>
</p>
<p></p>
<p>I <span style="font-size: 12pt;">apologize for the confusion. I</span><span style="font-size: 12pt;"> am splitting a fasta </span><span style="font-size: 12pt;">f</span><span style="font-size: 12pt;">ile that contains</span><span style="font-size: 12pt;"> approximately </span><span style="font-size: 12pt;">100,</span><span style="font-size: 12pt;">000
fasta sequences to 100</span><span style="font-size: 12pt;"> fasta </span><span style="font-size: 12pt;">files that contains 1000</span><span style="font-size: 12pt;"> sequences each. I am hoping this will expedite the BLASTx process. </span></p>
<p><br>
</p>
<p>Kind regards,<br>
</p>
<p><br>
</p>
<p>Zain<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Martin Gollery <mgollery@unr.edu><br>
<b>Sent:</b> Tuesday, May 5, 2015 10:23 AM<br>
<b>To:</b> Bio-Linux help and discussion<br>
<b>Subject:</b> Re: [Bio-Linux] Blasting Multiple Fasta Files</font>
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<div dir="ltr">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.
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<div>-Marty</div>
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<img height="1" width="1" style="display:none!important" src="http://t.signauxneuf.com/e1t/o/5/f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v4fhjlN5w6Cy8d75CPW3MxYkM3LvrVvW9c0Hhy1k1H6H0?si=4739913040265216&pi=c43afae0-b0cb-490e-ab7d-5ec17385ba62"></div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, May 5, 2015 at 7:00 AM, Zain A Alvi <span dir="ltr">
<<a href="mailto:zain.alvi@student.shu.edu" target="_blank">zain.alvi@student.shu.edu</a>></span> wrote:<br>
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<p>Dear Sir or Madam,<br>
</p>
<p><br>
</p>
<p>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. </p>
<p><br>
</p>
<p>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.<br>
</p>
<p><br>
</p>
<p>Sincerely,<br>
</p>
<p><br>
</p>
<p>Zain<br>
</p>
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-- <br>
<div class="gmail_signature">-- <br>
Martin Gollery<br>
Senior Bioinformatics Scientist<br>
Tahoe Informatics<br>
<a href="http://www.bioinformaticist.biz" target="_blank">www.bioinformaticist.biz</a><br>
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