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HMMER
User's Guide
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Dept. of Genetics |
WashU |
Medical School |
Sequencing Center |
CGM |
IBC|
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Eddy lab |
Internal (lab only) |
HMMER |
PFAM |
tRNAscan-SE |
Software |
Publications
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Next: Other profile HMM implementations
Up: Introduction
Previous: Command line options
HMMER is built to coexist peacefully with the BLAST suite of database
search programs [Altschul, 1991]. HMMER reads the following
environment variables (the examples given use UNIX csh syntax):
- [BLASTDB] Location of sequence databases that
hmmsearch will look in, in addition to the current
working directory.
Multiple directories are allowed, separated by colons. A
trailing slash on each path is important to BLAST, but not to HMMER.
Examples:
> setenv BLASTDB /nfs/databases/
> setenv BLASTDB /nfs/databases/:/nfs/moredatabases/
- [BLASTMAT] Location of substitution matrices that
hmmbuild -pam (the PAM prior option) can read.
Although HMMER can parse a colon-separated list, BLAST must
have a single directory path here.
Example:
> setenv BLASTMAT /nfs/databases/matrix/
- [HMMERDB] Location of HMMs, PFAM, or other HMMER
specific data files. Any program that reads an HMM file
looks in both HMMERDB and the current working directory.
Multiple directories are allowed, colon-separated.
Examples:
> setenv HMMERDB /usr/local/lib/hmmer/
> setenv HMMERDB /usr/local/lib/hmmer/:/nfs/databases/pfam/
Next: Other profile HMM implementations
Up: Introduction
Previous: Command line options
Direct comments and questions to <eddy@genetics.wustl.edu>