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<TITLE>RE: [BiO BB] custom blast server</TITLE>
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<P><FONT SIZE=2>Well I have no problems using the NCBI BLAST, but does it run as a HTTP service out of the box? or do I need to wrap it on some server code? my main problem is that I am not interested in returning high scoring sequences, rather I need to get another value associateed to the high scoring sequences and return a file. That is where arrangement is custom.</FONT></P>
<P><FONT SIZE=2>- Joel</FONT>
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<P><FONT SIZE=2>-----------------------------------</FONT>
<BR><FONT SIZE=2>Honestly, no. From the best I can figure out, you have an application</FONT>
<BR><FONT SIZE=2>and a BLAST server that are running on separate machines across the</FONT>
<BR><FONT SIZE=2>internet. You want the BLAST server to be able to handle multiple</FONT>
<BR><FONT SIZE=2>requests concurrently, and you have a relational database of sequences</FONT>
<BR><FONT SIZE=2>that you want to BLAST against.</FONT>
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<P><FONT SIZE=2>The standard way to do this is to run BLAST over HTTP, and fork an</FONT>
<BR><FONT SIZE=2>instance of the executable for every run. You'll get less performance</FONT>
<BR><FONT SIZE=2>than a persistant multi-threaded one, but I don't think that's how</FONT>
<BR><FONT SIZE=2>NCBI BLAST is written. And anyway, the bottleneck is going to be the</FONT>
<BR><FONT SIZE=2>database searches, not the process forking.</FONT>
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<P><FONT SIZE=2>I think Iddo asked a good question, and I'm also wondering about the</FONT>
<BR><FONT SIZE=2>requirement to be run off the SQL database. I'm not sure what that</FONT>
<BR><FONT SIZE=2>has to do with threading and XML RPC.</FONT>
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<P><FONT SIZE=2>Jeff</FONT>
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