<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.<div><br></div><div>-Marty</div><div><br></div><img src="http://t.signauxneuf.com/e1t/o/5/f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v4fhjlN5w6Cy8d75CPW3MxYkM3LvrVvW9c0Hhy1k1H6H0?si=4739913040265216&pi=c43afae0-b0cb-490e-ab7d-5ec17385ba62" style="display:none!important" height="1" width="1"></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><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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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></blockquote></div><br><br clear="all"><div><br></div>-- <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><a href="http://www.hiddenmarkovmodels.com" target="_blank">www.hiddenmarkovmodels.com</a><br><br></div>
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