IUBio

Webblast v0.97, a command line client to use blast 2.08 at NCBI.

Alex Dong Li lidong at globalserve.net
Thu May 20 21:02:00 EST 1999


Hello, there,

webblast (ver 0.97, 05/20/99), written in perl, does NCBI blast search 
(version 2.0.8) batchwise by acting as a www client (such as Netscape and IE) 
from the unix command line, and saves the results as local files in HTML 
and/or plain text. All options which are available from NCBI's web interface 
are available from command line. The old version (0.94) is still available. 
Both can be found at the following URL: 
http://www.genet.sickkids.on.ca/bioinfo_resources/software.html#webblast

Here is the list of new features: 
1) the sequences longer than the maximum length will be splitted first and the 
smaller fragments will be used to blast. To disable automatic splitting, add 
"-split=off". 
2) new option "-overlap=integer" sets the overlapping length of smaller 
fragments if the long sequences are splitted.
3) new option "-organism=name|number_representation" allows to limit database 
for searching. 
4) new option "-matrix=number_representation" allow to use a different scoring 
matrix. 
5) updated to use new version 2.0.8 of BLAST at NCBI. 

This new improved verion should be back version compatible if the new option 
"-split=off" is used and maximum length is set to 30000 (default is 10000 now 
to minimize occurrence of "CPU limit reached"). 

Here is the list of some other features: 
1) runs on all unix, Windows NT/9x--see installation instructions in the file.
2) very easy to install; 
3) can retrieve the graphical overview; 
4) some useful options: -default (same as -notask), -silent, -help, -test -log
5) Some important options are available in interactive mode; 
6) can use list file. 

To get help, enter "webblast -help".

Regards,

Alex.




More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net