mirror of https://github.com/tLDP/LDP
34 lines
1.2 KiB
Plaintext
34 lines
1.2 KiB
Plaintext
<CHAPTER ID="Bio ">
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<TITLE>BioInformatics and openMosix</TITLE>
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<SECT1><TITLE>Introduction</TITLE>
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<PARA>
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<indexterm><primary>blast</primary></indexterm>
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</PARA>
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</SECT1>
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<sect1><title>Blast</title>
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<para>
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One of the more frequent used application in this field is Blast,
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<ulink url="http://stl.bioinformatics.med.umich.edu/software/OM_BLAST_patch/openmosixpatch.html">
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<citetitle>Blast has a patch available that makes it work smoother
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</citetitle></ulink>
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with openMosix, but that's not the only alternative.
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</para>
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<para>First of all there are some known problems with this patch, and other
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versions of blast , blast tends to segfault sometimes, this mostly happens
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with the preformatted databases you download from the internet.
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If you run formatdb on a raw database these errors tend to go away.
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</para>
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<para>Next to the openMosix blast patch a lot of people run <ulink
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url="http://mpiblast.lanl.gov/"><citetitle>MPIBlast</citetitle></ulink>
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Given the fact that openMosix tends to speed up MPI, adding openMosix to this
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config might even give you more power for your money, however we will have to
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do some extra research to be able to confirm this.
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</para>
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</sect1>
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<!-- ClustalW, Fasta ...etc -->
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</CHAPTER>
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