In addition to our HMM-based Pfam entries (Pfam-A), we used to make a set of automatically generated, non-HMM based entries called Pfam-B. The Pfam-B entries were derived from clusters generated by applying the ADDA algorithm to an all-against-all BLAST search of UniRef-40, and removing any regions covered by Pfam-A. The overhead of producing Pfam-B in this way became too great, and as of Pfam 28.0, we stopped making Pfam-B entries (see [1] for a longer discussion on why we stopped producing Pfam-B). Erik Sonnhammer has devised an alternative method of making Pfam-B using the MMSeqs2 software [2], and an overview of the process is given below (more details will follow in the next Pfam paper).
We have already begun to use the new version of Pfam-B to generate new families, and 11 of these are in Pfam 33.1. For example, the TUTase family (PF19088) was built using Pfam-B as the source. We expect that Pfam-B will be a very useful source of additional families in the coming years.
How the new Pfam-B was created
UniProtKB sequences not covered by Pfam-A were clustered using MMSeqs2 and multiple sequence alignments of each cluster were generated with FAMSA [3]. This resulted in 136730 Pfam-B families that on average contain 99 sequences (max 40912) and are 310 positions wide (max 29216).
How to access the new Pfam-B
The Pfam-B alignments are released as a tar archive on the Pfam FTP site [Pfam-B.tgz]. We do not plan to integrate them into the Pfam website, but we will generate them for each future Pfam release.
Posted by Erik Sonnhammer and the Pfam team
References
1. Finn et al. (2015) The Pfam protein families database: towards a more sustainable future.
2. Hauser et al. (2016) MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
3. Deorowicz et al. (2016) FAMSA: Fast and accurate multiple sequence alignment of huge protein families
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