Question: Is the source code for the NCBI-BLAST service available anywhere?
3
gravatar for Jeff Wintersinger
5.6 years ago by
Calgary, AB
Jeff Wintersinger60 wrote:

Hello!

Is the source code for the NCBI-BLAST service available anywhere? In particular, I'm interested in producing the visualization NCBI-BLAST offers, such as the one below, using BLAST results from my own installation. I have searched for the source, but can't find it -- it doesn't seem to be included in the BLAST+ tarball, nor can I find it elsewhere on the NCBI FTP site.

Thank you!

blast ncbi • 4.1k views
ADD COMMENTlink modified 3.2 years ago by rpavez0 • written 5.6 years ago by Jeff Wintersinger60

Have u checked this link. Its says the source code is available here. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.29+-src.zip seems to be the link to download source code.

ADD REPLYlink written 5.6 years ago by Ashutosh Pandey11k

Thank you for the suggestion. I've looked through the BLAST+ source in some detail in trying to find the web frontend and visualization code, but to no avail. In particular, I can't find any file named Blast.cgi (which appears on the NCBI BLAST web site). Grepping the source for the string "Blast.cgi" or any one of a number of strings that appear in the page source doesn't yield meaningful results, either. As such, the code I'm looking for either isn't included with BLAST+, or is extremely well-hidden.

ADD REPLYlink written 5.6 years ago by Jeff Wintersinger60
6
gravatar for Neilfws
5.6 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I am reasonably sure that code for the NCBI web interface to BLAST is no longer distributed with BLAST+.

It is still available for the older version of BLAST; the "latest" release (2011) is here: ftp://ftp.ncbi.nih.gov/blast/executables/release/LATEST. Look for the files that begin "wwwblast", but note that the code is not maintained and may be tricky to install.

There are a few other web interfaces to BLAST around (try Google search) which might provide what you want.

ADD COMMENTlink written 5.6 years ago by Neilfws48k

Thank you! I suspected as much, but your confirmation helps. I'll e-mail the NCBI people to be doubly sure.

ADD REPLYlink written 5.6 years ago by Jeff Wintersinger60
0
gravatar for Dr. Mabuse
5.2 years ago by
Dr. Mabuse47k
Bergen, Norway
Dr. Mabuse47k wrote:

A similar visualization can be achieved with the Bio::GMOD::Blast::Graph module. A similar simple interface can be implemented in pure perl by adapting BlastGraphicViewer.

ADD COMMENTlink written 5.2 years ago by Dr. Mabuse47k
0
gravatar for rpavez
3.2 years ago by
rpavez0
rpavez0 wrote:

Required files are in ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.14/blast-2.2.14-x64-linux.tar.gz (VERY OLD VERSION, newer ones doesn't include www tool) Apache config: http://blog.pansapiens.com/2008/08/25/setting-up-wwwblast-on-ubuntu-apache/

ADD COMMENTlink written 3.2 years ago by rpavez0
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