HMMER User's Guide

| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC| | Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

Environment variable configuration

These steps are optional, and will only apply (I think) to sufficiently POSIX-compliant operating systems like UNIX, Linux, or WinNT.

HMMER reads four environment variables, and is designed to coexist peacefully with an installation of WUBLAST or NCBI BLAST:

BLASTDB

- directory location of FASTA-formatted sequence databases

BLASTMAT

- directory location of BLAST substitution matrices

HMMERDB

- directory location of HMM databases (e.g. PFAM)

HMMER_NCPU

- maximum number of CPUs to utilize in a multiprocessor

If you have installed BLAST, you probably already have the two BLAST environment variables set in system-wide or user-specific .cshrc files.

All four variables 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