NCBI toolkit (incl. blast) on clx e sp5

[Andrew Emerson]

Dear all

We have installed the latest version of the NCBI toolkit, version 2.2.11,
on clx and sp5.
In order to use any of the programs in the toolkit load the ncbi module as
usual. For example,

module load ncbi

and then you can use blastall, formatdb, fastacmd etc directly from the
command line.

A couple of pre-formatted genomic databases,  EST human and human_genomic,
are also available and can be found in the directory $BLASTDB. Thus for
example to run a blast alignment of sequences in seq.dat against the human
EST database,

blastall -p blastn -i seq.dat -d $BLASTDB/est_human

For more information there is a UNIX man page for each command, e.g. man
blastall, while of course the NCBI (http://www.ncbi.nlm.nih.gov/) remains
the definitive guide.

best wishes
Andy Emerson


------------------------
Dr Andrew Emerson
CINECA (High Performance Systems)
via Magnanelli, 6/3
40033 Casalecchio di Reno (BO)-ITALY
tel: +39-051-6171653, fax: +39-051-6132198
e-mail: a.emerson a cineca.it