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Hi Steven, |
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|
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You're looking for the package sci-biology/ncbi-tools. There are |
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tutorials available online for setting that package up for local BLAST |
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searches. The basic steps are: |
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|
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1. Decide which type of BLAST you're going to run, and which database |
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you're going to search against. |
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2. If it's one of the standard NCBI databases, download it from the |
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NCBI FTP site. If you have your own set of sequences that you wish to |
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compile into a database, use the formatdb and fastacmd utilities to |
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make the database. |
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3. Run the search. Unless you have massive amounts of data, there's no |
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need to worry about MPI or other parallelization. BLAST has a minor |
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parallelization speed-up built in through a -a option which should be |
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set to your number of cores. MPIBLAST is an addition to BLAST for |
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high-performance cluster environments, and is non-trivial to set up. |
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|
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-ak |
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|
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|
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On Tue, Jul 28, 2009 at 10:52, Steven Lembark<lembark@×××××××.com> wrote: |
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> |
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> Need to comopare some results of another comparision |
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> method to blast (or fasta). I think that the proper |
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> packge to install would be: |
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> |
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> sci-biology/mpiblast |
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> |
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> given that 'emerge --search fasta' got me nada. |
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> |
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> Q: Anyone have any experience setting the beast |
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> up and sumitting jobs to it? |
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> |
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> Any pointers would be greatly appreciated as I have |
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> to start producing results rather quickly for some |
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> work on an HIV project. |
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> |
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> We need to start validating results of comparing |
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> pseudo-species of HIV with blast and W-Curve |
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> techniques to speed up cataloging the beasties. |
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> |
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> thanx |
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> |
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> -- |
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> Steven Lembark 85-09 90th St. |
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> Workhorse Computing Woodhaven, NY, 11421 |
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> lembark@×××××××.com +1 888 359 3508 |
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> |
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> |