[Bioclusters] BLAST input files for high throughput facility

Mon, 9 Feb 2004 16:32:12 -0000

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Hi,

I am in the process of setting up a BLAST service on our local compute =
cluster, which uses OpenPBS, and I am planning to do this through a grid =
front end (GT3 grid service).=20

I was wondering how other people deal with the formatting of BLAST =
databases in this sort of setting. Normally, one would have to run the =
formatdb facility on the BLAST database before you can do your search =
but this is tedious and I wonder how long it would take to run this over =
the whole of the human genome, say (I haven't actually tried it yet).=20

Either way, is there any way of getting round formatdb? We would =
possibly like to blast datasets that are dynamically composed at =
runtime, following an SQL query into a live database. Has anyone done =
this sort of thing?

cheers

Micha

--------------------------------------------------=20
Dr Micha M Bayer
Grid Developer, Bridges Project
National eScience Centre, Glasgow Hub
246c Kelvin Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
Email: michab@dcs.gla.ac.uk
Project home page: http://www.brc.dcs.gla.ac.uk/projects/bridges/
Personal home page: http://www.brc.dcs.gla.ac.uk/~michab/

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<P><FONT SIZE=3D2>Hi,<BR>
<BR>
I am in the process of setting up a BLAST service on our local compute =
cluster, which uses OpenPBS, and I am planning to do this through a grid =
front end (GT3 grid service).<BR>
<BR>
I was wondering how other people deal with the formatting of BLAST =
databases in this sort of setting. Normally, one would have to run the =
formatdb facility on the BLAST database before you can do your search =
but this is tedious and I wonder how long it would take to run this over =
the whole of the human genome, say (I haven't actually tried it =
yet).<BR>
<BR>
Either way, is there any way of getting round formatdb? We would =
possibly like to blast datasets that are dynamically composed at =
runtime, following an SQL query into a live database. Has anyone done =
this sort of thing?<BR>
<BR>
cheers<BR>
<BR>
Micha<BR>
<BR>
--------------------------------------------------<BR>
Dr Micha M Bayer<BR>
Grid Developer, Bridges Project<BR>
National eScience Centre, Glasgow Hub<BR>
246c Kelvin Building<BR>
University of Glasgow<BR>
Glasgow G12 8QQ<BR>
Scotland, UK<BR>
Email: michab@dcs.gla.ac.uk<BR>
Project home page: <A =
HREF=3D"http://www.brc.dcs.gla.ac.uk/projects/bridges/">http://www.brc.dc=
s.gla.ac.uk/projects/bridges/</A><BR>
Personal home page: <A =
HREF=3D"http://www.brc.dcs.gla.ac.uk/~michab/">http://www.brc.dcs.gla.ac.=
uk/~michab/</A><BR>
<BR>
</FONT>
</P>

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