I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete: http://www.ncbi.nlm.nih.gov/books/NBK52637/
Relevant information:
BLAST version: 2.2.29+
User Variable Setting:
BLASTDB
C:\Program Files\NCBI\blast-2.2.29+\bin
System Variable Setting:
BLASTDB
C:\Program Files\NCBI\blast-2.2.29+\bin
Both the machine's user and system path variables include the full path above. Since I have obviously never done this previously, do I need to create a local database? Is there a current tutorial which describes the procedure in a concise and "neophyte friendly" fashion? Once properly configured, are the results identical to NCBI's blas, e.g., red alignment bars, etc?
There's a great guide here that's neophyte-friendly: http://openwetware.org/wiki/Wwwblast - unfortunately It's tailed for MacOS but if you install csh (a shell) and apache (web server) on your Windows machine, it's easy enough to follow. I don't know of any comparable guides to set up BLAST on Windows.
The results are pretty much NCBI's blast once set up.
If you don't have apache or some other webserver running on your local machine, I'd download WAMP (windows, apache, mysql, php stack) which is "a bunch of stuff you need to host/run a (local) website on your computer" all in one package. Then, set up NCBI's blast as you would a normal website - throw it in www or wherever WAMP hosts it from, modify the apache config file as per the tutorial (find it in your wamp's apache install somewhere), create the custom databases and add them to the drop-down box as per the tutorial (just remember to modify blast.rc in the end as per the tutorial).. The only "local" DB you need to set up is the BLAST databases with makeblastdb. I still think you should find the above guide very helpful even though it's geared for Mac OS, and if you figure out how to get WAMP going, you don't need to fuss about with installing a shell on your windows box to follow the guide letter-by-letter: just treat BLAST as any other locally-hosted website.
Just a comment, but I found the makeblastdb command to be rather picky in blast 2.2.29+ and rolled back to 2.2.28+. What worked before, no longer worked, etc.
Just a comment, but I found the makeblastdb command to be rather picky in blast 2.2.29+ and rolled back to 2.2.28+. What worked before, no longer worked, etc.