Webblast--a program to do gapped blast from unix command line
webblast, written in perl, does NCBI gapped blast search (version 2)
by mimicing a www client (such as Netscape &IE) from the unix
command line, and saves the results as local files.
Most options are similar to those available from NCBI blast page.
Currently the graphical overview is not available.
Some examples are:
webblast -format=fasta sample1.seq
webblast -prog=blastn -datab=nr -align=25 -notask
webblast -prog=blastp -datab=swissprot -email=smith at dept.univ.edu
Input sequence file(s) can be in GCG, fasta or plain text format .
(you need to specify by "-format=fasta" or "-format=text" if files
are in last two formats). If no filename is specified,
all files in current directory will be blasted.
It is available at
http://www.genet.sickkids.on.ca/bioinfo_resources/software.html
To install the program 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 postclient.pl to your system,
2) change the file permissions so that you can run them,
3) modify the two files according to the instruction in the headers
If you have any suggestions/comments, please let me know.
Regards,
Alex Dong Li
