PfamDB-Sapelo2

A database for Hmmer and Pfam_scan program

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). In some releases Pfam includes both Pfam-A and Pfam-B. Because the entries in Pfam-A do not cover all known proteins, a supplement was provided called Pfam-B. Although of lower quality, Pfam-B families could be useful when no Pfam-A families were found. Pfam-B has been discontinued and reintroduced in various releases.

More information about Pfam can be found at the Pfam website

There are multiple versions under /db/pfam The Pfam database must be formatted to work with certain software such as HMMER or Pfam_scan. The non-formulated downloads are numbered with the version of the Pfam database.The currently available versions are 27.0 33.0 and 34.0. The versions which have been formatted to work with HMMER are listed with the Pfam version followed by the HMMER version they have been formatted for. The currently available versions are 27.0-hmmer3.0 and 34.0-hmmer3.3.2.

/db/pfam/

The commands to generate the data is documented at the UGA file sitting at the same directory with data:

formatdb -i Pfam-A.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
formatdb -i Pfam-B.fasta -n Pfam-A -t Pfam-A -l Pfam-A.log -p T
ml HMMER/3.1b2-foss-2016b
hmmpress Pfam-A.hmm
hmmpress Pfam-B.hmm
ml WU-Blast/2.2.6-foss-2016b
xdformat -p -x Pfam-A.fasta
xdformat -p Pfam-B.fasta

If you would like a particular version of the Pfam database to work with a particular version of HMMER you can download or prepare this database yourself. To format Pfam for use with HMMER you can use the function, hmmpress, which comes built into HMMER. The hmmpress step is required for hmmscan to work. The following commands can be used to prepare pfam.hmm data.

ml HMMER/3.1b2-foss-2016b #use whichever version of HMMER you would like to use for hmmscan
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz #wget which ever version of Pfam you would like
gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm

version built with hmmer 3.0 (Pfam_scan friendly)

/db/pfam/27.0-hmmer3.0/Pfam-A
/db/pfam/27.0-hmmer3.0/Pfam-B
/db/pfam/27.0-hmmer3.0/Pfam-A.hmm
/db/pfam/27.0-hmmer3.0/Pfam-B.hmm

Databases are download install files from sanger website.