Blast

Blast is the BLAST search automator written in C++. Annotator used to go to web page called "BLAST"(http://www.ncbi.nlm.nih.gov/blast/blast.cgi), enter data from a BMRB deposition(STAR file), and then take the results and insert relevant data into deposition. Blast automated these steps.

 

1. How Blast works.

Blast acts like a pseudo web browser. First, it gets sequence and other necessary data from the input starfile. Then it queries the BLAST site with this data, by opening a socket to the BLAST server, and speaking in HTTP protocol. Then it parses the returned web page for the relevant data and finally inserts this data into the deposition. Now blast runs itself once a week by cron through all the starfiles in /bmrb/htdocs/data_library/files.

2. How to use Blast.

Even though blast automatically updates starfiles once a week, it can be used with one starfile on command line by typing

%/bmrb/bin/blast [-q] [-seqdet] [-ow] <inputfile> [id]

 

Blastrc file

On startup blast will try to read a configuration file; default is /bmrb/etc/blastrc (defined in Makefile). Blastrc file contains usual key = value pairs, one per line. Valid keys are

Lines that don't start with either of those are ignored. Keys are case-insensitive, whitespace (spaces and/or tabs) around = is ignored. Default values are set at compile-time in the Makefile.
NOTE: as far as blast is concerned, value is everything between the first non-whitespace character after the = and the end of line ('\n'). Make sure there's a newline right after the value. Also make sure that value is less than 512 characters long.

3. Note.

  1. Blast is dependent upon the BLAST site. If the BLAST site changes its interface, this will probably break this program.
  2. When blast runs, it generates two files in currently working directory. One is "query_file" for query string submitted to the BLAST server, the other is "blast_out" which is returned web page containg blast search result from the BLAST server.