mirror of
https://git.FreeBSD.org/ports.git
synced 2024-10-29 21:39:24 +00:00
91f5c278fe
Profile hidden Markov models for biological sequence analysis. PR: 7120 Submitted by: Matthew Jason Euclid Barnhart <barnhart@sequencer.wustl.edu>
23 lines
884 B
Plaintext
23 lines
884 B
Plaintext
*********************************************************
|
|
|
|
Note on environment variables:
|
|
|
|
HMMER reads three environment variables:
|
|
HMMERDB - directory location of HMM databases (e.g. PFAM)
|
|
BLASTDB - directory location of FASTA-formatted sequence databases
|
|
BLASTMAT - directory location of PAM scoring matrices
|
|
|
|
If you have installed BLAST, you probably already have these
|
|
environment variables set in system-wide or user-specific
|
|
.cshrc files. They are optional. If they are set up, you
|
|
can simplify command lines to:
|
|
> hmmpfam pfam my.query
|
|
> hmmsearch my.hmm swiss35
|
|
instead of
|
|
> hmmpfam /some/long/path/to/databases/pfam my.query
|
|
> hmmsearch my.hmm /some/long/path/to/databases/swiss35
|
|
|
|
Please see the website http://hmmer.wustl.edu/ for more information.
|
|
|
|
*********************************************************
|