Blast Shell Wanted

brutlag at cmgm.stanford.edu brutlag at cmgm.stanford.edu
Tue Oct 27 12:50:12 EST 1992


In article <1992Oct26.150840.16405 at ms.uky.edu> jmg at seqanal.mi.uky.edu (Joel
Guthridge) writes:
>	Has anyone created a Unix Shell to provide easier interfacing to the BLAST
>programs?  I'm looking for something that will ask the user for the necessary
>information to carry out the search, ie. seq. file, output file, databases to
search, etc.

Joel,

	We have a series of BLAST and FASTA scripts both for users and for Unix
systems administrators who prepare BLAST indexes available via anonymous FTP. 
The database indexing scripts are specific for those who use the
IntelliGenetics suite  (IntelliGenetics, FastA and BLAST all use the same
database format) but the BLAST and FASTA user shells can be used on any Unix
system.  You only have to change the paths for the directories containing the
databases from /usr/igsw/aa and /usr/igsw/na to wherever you store your
databases and BLAST indexes.  These scripts give users access to the most
commonly changed variables.  Full access to all command line parameters can be
added easily.

	These files are available by anonymous ftp at cmgm.stanford.edu in the
directory pub/IGdb.  Read the README file for an explanation of all scripts and
data files for BLAST and FASTA.  The scripts set-up FASTA and BLAST for
searching GenBank and subdivisions of GenBank, UEMBL, Swiss-Prot, PIR, AIDS and
GenPept (FASTA only).

Doug Brutlag




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