Dear Zain<div><br></div><div>It would still take time. Should you use queuing or mpich, it should make your tasks done easy. Above all, it all depends on how good the configuration is.</div><div><br></div><div>Regards</div><div>Prash<br><br>On Tuesday, May 5, 2015, Zain A Alvi <<a href="mailto:zain.alvi@student.shu.edu">zain.alvi@student.shu.edu</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
<div style="color:rgb(0,0,0)">
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Martin Gollery <<a href="javascript:_e(%7B%7D,'cvml','mgollery@unr.edu');" target="_blank">mgollery@unr.edu</a>><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>
<div> </div>
</div>
<div>
<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 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="javascript:_e(%7B%7D,'cvml','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">
<div dir="ltr">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<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>
</div>
</div>
<br>
_______________________________________________<br>
Bio-Linux mailing list<br>
<a href="javascript:_e(%7B%7D,'cvml','Bio-Linux@nebclists.nerc.ac.uk');" target="_blank">Bio-Linux@nebclists.nerc.ac.uk</a><br>
<a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>-- <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>
</div>
</div>
</div>
</div>
</div>
</blockquote></div><br><br>-- <br><p><br>Sent from iPad Mini<br></p>