IUBio

how to get a local copy of "pairwise blast"?

Joe Ryan jfryan at NHGRI.NIH.GOV
Tue Jun 22 22:22:18 EST 1999


> Does anyone know where I can get some info of getting or building a
> local copy of "pairwise blast" program?

Guang,

You could right a script that will format one of the sequences
using the formatdb program and then run a BLAST

   formatdb $SEQ_A
   blastall -p blastp -d $SEQ_A -i $SEQ_B

Or you could use FASTA (ftp://ftp.virginia.edu/pub/fasta/)
   which allows you to compare any 2 FASTA formatted files with 1 or more 
   sequence (no formatting required).
   lalign is also included in this package.

Or you could use GCG. 
Gap, BestFit, and FrameAlign all do pairwise comparison.
Compare, DotPlot, GapShow will give you graphical representations.

you could also have a look at crossmatch and swat from the Phrap package
 http://bozeman.mbt.washington.edu/index.html

Good Luck,

Joe 
--
Joseph Ryan
Programmer
National Human Genome Research Institute

On Tue, Jun 22, 1999 at 09:52:33PM +0000, gmei at my-deja.com wrote:
> Hi:
> 
> Does anyone know where I can get some info of getting or building a
> local copy of "pairwise blast" program?
> 
> NCBI does offer web interface to run "pairwise blast" at
> http://www.ncbi.nlm.nih.gov/gorf/bl2.html,
> but we need to to run this on our own Digital Alpha Unix Server.
> 
> Does "gcg" offer the capability?
> Does Washington Univ. Blast package have this kind of function?
> 
> If you reply, please send a copy to gmei at pavonis.com
> 
> Thanks for your help.
> 
> Guang Mei
> gmei at 3rdmill.com
> http://www.3rdmill.com
> 
> 
> Sent via Deja.com http://www.deja.com/
> Share what you know. Learn what you don't.
> 




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