How do I run blast searches in batch mode?
After NCBI replaced their experimental blast servers in Jan 98, the
blast searches on the helix system changed. The new blast program
does not have the 'blast -batch' command. Instead, you should
use the helix utility
batchblast. A simple run of batchblast would be
helix% batchblast *.seq
which would run blast searches with default parameters for each
of the files called xxx.seq, and produce an output file called
xxx.blastn for each search. Batchblast has options to choose
the database, program, and parameters; see
the batchblast man page for more information.