WEBBLAST (Improved)--do new & old NCBI blast from command line

[Alex Dong Li]

WEBBLAST (Improved)--do new & old NCBI blast from command line

Upon the suggestions from some users, we have improved webblast which we 
announced a few days ago.

webblast and webblastv1, written in perl, do new NCBI blast search (gapped, 
version 2.x.x) and old NCBI blast search (version 1.x.x), respectively, by 
mimicing a www client (such as Netscape and IE) from the unix command line, 
and save the results as local files in HTML and/or plain text. Most options 
are similar to those available from NCBI blast page. Currently the graphical 
overview of new NCBI blast search is not available.

Some examples of webblast are:
webblast 
webblast -align=25 -html=off -notask s1.seq s2.seq s3.seq
webblast -prog=blastp -datab=swissprot -email=smith at univ.edu *.seq

Some examples of webblastv1 are:
webblastv1 
webblastv1 -align=default -html=off -notask s1.seq s2.seq s3.seq
webblastv1 -prog=blastp -datab=swissprot -email=smith at univ.edu *.seq

Input sequence file(s) can be in GCG, fasta or plain text format. You can use 
the wildcards (* and ?) to spicify a group of files, or list them 
individually. If no filename is specified, all files in current directory will 
be blasted. 

Programs are available freely at:
http://www.genet.sickkids.on.ca/bioinfo_resources/software.html

It should be very easy to install the programs. If you know a little bit about 
unix, you do not even need help from your system admin.
To install the programs on your own machine,
   0) install perl for unix (For most networked unix machines, perl
        should have been installed. If not, contact your system admin),
   1) copy webblast and/or webblastv1, and postclient.pl to your system.
        All files are ASCII files. You can simply use your web browser
        to save them as local files. 
   2) change the file permissions so that you can run them,
   3) modify the files according to the instructions in the header of
        each file.

BTW, webblastv1 is still a beta version. If you have any suggestions/comments, 
please let us know.

Regards,

Alex Dong Li