Pfam SARS-CoV-2, special release -------------------------------- v1.0 02/04/2020 We have reviewed all of the Pfam entries that match against the proteins encoded by SARS-CoV-2, and added a few additional entries to provide as comprehensive set of annotations as possible. We have improved the naming consistency of these Pfam entires and updated the descriptions. As this is a special release of Pfam, these updates are not yet available on the Pfam website. We anticipate making them available in 6-8 weeks. The files currently available are: 1. Pfam-A.SARS-CoV-2.hmm - this is the mini Pfam HMM library. 2. matches.scan - the matches to SARS-CoV-2 using hmmscan. 3. covid-19.fasta - the SARS-CoV-2 proteins from UniProt. How to use this library? ------------------------ This library is not compatible with the pfam_scan software that we normally recommend to reproduce Pfam matches, as this library only contains a small subset of models. If you wish to compare these models to your own sequences, please use the following HMMER commands: $ hmmpress Pfam-A.SARS-CoV-2.hmm This only needs to be performed once. Then to compare your sequences (in a file called my.fasta) to this special Pfam profile HMM library, then: $ hmmscan --cut_ga --domtblout matches.scan Pfam-A.SARS-CoV-2.hmm my.fasta The --domtblout option enables you to save the matches in a more convenient tabular form, if you do not want to parse the HMMER output.