Batch BLAST

Stephane Bortzmeyer bortzmeyer at pasteur.fr
Wed Jul 28 02:59:05 EST 1999


In article <cupton-2707991459320001 at hera.bioc.uvic.ca>,
 cupton at uvic.ca (Chris Upton) writes:

>    Is there a simple way to send off 200 blast searches to NCBI or other
> server and have them return the results in HTML or text format?

I see two solutions:

- write a Web client which will automatize the task. If you like Perl, 
  see "Web client programming with Perl" by Clinton Wong (O'Reilly), which
  is a good book and has similar examples. For the HTMl translation, your
  program can then call any translator like Html4blast 
  <ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/Blast_tools/Html4blast/>

- install Blast on your machine. It is a bit painful but possible. The real
  problem is not the program but the banks. If you want to maintain an
  uptodate copy of Genbank, it is painful. Well, if you want, you have
  packages of Blast for Debian 
  <http://www.pasteur.fr/units/sis/debian/biology-en.html> and RedHat 
  <http://rpmfind.net/linux/RPM/Applications_Bioinformatics.html>. This
  solution will allow you to script at will and to run your 200 searches
  very easily.





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