[gentoo-science] Setup/configure blast server?

[gentoo-science] Setup/configure blast server?

[Steven Lembark]

Need to comopare some results of another comparision
method to blast (or fasta). I think that the proper
packge to install would be:

    sci-biology/mpiblast

given that 'emerge --search fasta' got me nada.

Q: Anyone have any experience setting the beast
   up and sumitting jobs to it?

Any pointers would be greatly appreciated as I have
to start producing results rather quickly for some
work on an HIV project.

We need to start validating results of comparing 
pseudo-species of HIV with blast and W-Curve 
techniques to speed up cataloging the beasties. 

thanx

-- 
Steven Lembark                                          85-09 90th St.
Workhorse Computing                               Woodhaven, NY, 11421
lembark@wrkhors.com                                    +1 888 359 3508

Re: [gentoo-science] Setup/configure blast server?

[Andrey Kislyuk]

Hi Steven,

You're looking for the package sci-biology/ncbi-tools. There are
tutorials available online for setting that package up for local BLAST
searches. The basic steps are:

1. Decide which type of BLAST you're going to run, and which database
you're going to search against.
2. If it's one of the standard NCBI databases, download it from the
NCBI FTP site. If you have your own set of sequences that you wish to
compile into a database, use the formatdb and fastacmd utilities to
make the database.
3. Run the search. Unless you have massive amounts of data, there's no
need to worry about MPI or other parallelization. BLAST has a minor
parallelization speed-up built in through a -a option which should be
set to your number of cores. MPIBLAST is an addition to BLAST for
high-performance cluster environments, and is non-trivial to set up.

-ak


On Tue, Jul 28, 2009 at 10:52, Steven Lembark<lembark@wrkhors.com> wrote:
>
> Need to comopare some results of another comparision
> method to blast (or fasta). I think that the proper
> packge to install would be:
>
>    sci-biology/mpiblast
>
> given that 'emerge --search fasta' got me nada.
>
> Q: Anyone have any experience setting the beast
>   up and sumitting jobs to it?
>
> Any pointers would be greatly appreciated as I have
> to start producing results rather quickly for some
> work on an HIV project.
>
> We need to start validating results of comparing
> pseudo-species of HIV with blast and W-Curve
> techniques to speed up cataloging the beasties.
>
> thanx
>
> --
> Steven Lembark                                          85-09 90th St.
> Workhorse Computing                               Woodhaven, NY, 11421
> lembark@wrkhors.com                                    +1 888 359 3508
>
>