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<TITLE>RE: [BiO BB] custom blast server</TITLE>
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<P><FONT SIZE=2>Well,</FONT>
<BR><FONT SIZE=2> Here is the deal. I am assuming that you suggest that I dump all my sequences, format them, and use the BLAST executable provided by NCBI, right? I thought about that too. However, The application is going to make a BLAST request over the internet and the BLAST server needs to thread (so we can handle many concurrent connections) and return the BLAST results to the application when the search is complete. I could make a wrapper type server in Perl, but I think that is a bad idea. I would like to have something cleaner. Ideally I would like to have a Threading server that handles BLAST requests via XML RPC or something like that and integrates better with my application. Am I making any sense here?</FONT></P>
<P><FONT SIZE=2>- Joel</FONT>
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<P><FONT SIZE=2>-----Original Message-----</FONT>
<BR><FONT SIZE=2>From: Iddo Friedberg [<A HREF="mailto:idoerg@cc.huji.ac.il">mailto:idoerg@cc.huji.ac.il</A>]</FONT>
<BR><FONT SIZE=2>Sent: Wednesday, December 05, 2001 10:21 AM</FONT>
<BR><FONT SIZE=2>To: 'bio_bulletin_board@bioinformatics.org'</FONT>
<BR><FONT SIZE=2>Cc: Joel Dudley</FONT>
<BR><FONT SIZE=2>Subject: Re: [BiO BB] custom blast server</FONT>
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<P><FONT SIZE=2>Hi Joel,</FONT>
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<P><FONT SIZE=2>I do not know the answer to your specific question. However, I am a bit</FONT>
<BR><FONT SIZE=2>curious as to why you would like to run BLAST vs. an SQL database. You can</FONT>
<BR><FONT SIZE=2>easily convert any data you may have to a flat format fasta file, and then</FONT>
<BR><FONT SIZE=2>use NCBI tools formatdb to create the format which BLAST recognizes. A</FONT>
<BR><FONT SIZE=2>table which translates from your FFFF to the SQL key fields can correlate</FONT>
<BR><FONT SIZE=2>between the two, in case you have more than just sequence information in</FONT>
<BR><FONT SIZE=2>your SQL database.</FONT>
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<P><FONT SIZE=2>This is not a criticism of your choice of methods, I was just wondering</FONT>
<BR><FONT SIZE=2>what is the application demand that makes you want to take the trouble. I</FONT>
<BR><FONT SIZE=2>have toyed with the idea of doing something similar myself, but I always</FONT>
<BR><FONT SIZE=2>caved in and resorted to the method above.</FONT>
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<P><FONT SIZE=2>But hey, if you write up such a thing, that would be really cool!</FONT>
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<P><FONT SIZE=2>Yours,</FONT>
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<P><FONT SIZE=2>Iddo</FONT>
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<P><FONT SIZE=2>On Wed, 5 Dec 2001, Joel Dudley wrote:</FONT>
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<P><FONT SIZE=2>: Hello All,</FONT>
<BR><FONT SIZE=2>: I am creating a biological database for an application that I am working</FONT>
<BR><FONT SIZE=2>: on. The database contains cDNA and AA sequences among other things. My</FONT>
<BR><FONT SIZE=2>: application needs to perform a BLAST search on sequences in my database</FONT>
<BR><FONT SIZE=2>: only. I would like to create my own custom BLAST server that performs BLAST</FONT>
<BR><FONT SIZE=2>: searches on my PostgreSQL database. I planned on writing my own threading</FONT>
<BR><FONT SIZE=2>: BLAST server in Java but I was wondering if anyone know of some tools,</FONT>
<BR><FONT SIZE=2>: Classes, or libraries that would perform a BLAST onsequences in a</FONT>
<BR><FONT SIZE=2>: PostgreSQL DB. Any language is welcome. If there is something close that is</FONT>
<BR><FONT SIZE=2>: open-source I could modify the source to make it work I guess. Thanks.</FONT>
<BR><FONT SIZE=2>:</FONT>
<BR><FONT SIZE=2>: - Joel</FONT>
<BR><FONT SIZE=2>:</FONT>
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<P><FONT SIZE=2>--</FONT>
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<P><FONT SIZE=2>Iddo Friedberg | Tel: +972-2-6757374</FONT>
<BR><FONT SIZE=2>Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308</FONT>
<BR><FONT SIZE=2>The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il</FONT>
<BR><FONT SIZE=2>POB 12272, Jerusalem 91120 |</FONT>
<BR><FONT SIZE=2>Israel |</FONT>
<BR><FONT SIZE=2><A HREF="http://bioinfo.md.huji.ac.il/marg/people-home/iddo/" TARGET="_blank">http://bioinfo.md.huji.ac.il/marg/people-home/iddo/</A></FONT>
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