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<[email protected]> 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 > [email protected] +1 888 359 3508 > >
