Module Hmmer

source code

Search Hmmer Pfam database and retrieve conservation data.

Classes

HmmerError

HmmerdbIndex
Checks if the hmm database has been indexed or not, if not indexing will be done.

HmmerSearch
Search hmm database (using the hmmpfam program) with a sequence in fasta format.

HmmerProfile
Get the hmm profile with name hmmName from hmm databse (using the program hmmfetch).

HmmerAlign
Align fasta formated sequence to hmm profile (using hmmalign).

Hmmer
Search Hmmer Pfam database and retrieve conservation score for model

Test
Hmmer test

Variables

hmmpfamExe = settings.hmmpfam_bin

hmmfetchExe = settings.hmmfetch_bin

hmmalignExe = settings.hmmalign_bin

hmmindexExe = settings.hmmindex_bin

hmmDatabase = settings.hmm_db

Variables Details

Value:

settings.hmmpfam_bin

Value:

settings.hmmfetch_bin

Value:

settings.hmmalign_bin

Value:

settings.hmmindex_bin

Value:

settings.hmm_db