[WashU] 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 |

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

HMMERDB
- directory location of HMM databases (e.g. PFAM)
BLASTDB
- directory location of FASTA-formatted sequence databases
BLASTMAT
- directory location of BLAST substitution 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


next up previous contents
Next: Recommended systems Up: Installation Previous: Compiling from a source-only


Direct comments and questions to <eddy@genetics.wustl.edu>