HMMER is built to coexist peacefully with the BLAST suite of database search programs [1]. HMMER reads the environment variable BLASTDB to determine the location of the BLAST-formatted main sequence databases (Swissprot, Genbank) on your system. If BLASTDB is set (in your .cshrc or .login), you can call the search programs using only the name of the BLAST database, rather than the full cumbersome path to it.
In other words, rather than typing:
hmmsw my.hmm /usr/whatever/seqlibs/blast/swissyou can use:
hmmsw my.hmm swiss