Pfam SARS-CoV-2, special release 
--------------------------------

v2.0 06/04/2020
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We have now provided a more complete set of Pfam flatfiles, with one family, 
PF12124, renamed since the last release. This release still contains just 
the 40 entires that match the proteins encoded by SARS-CoV-2. In addition 
to the previously released files, we have made the following files available:

Pfam-A.SARS-CoV-2.seed - the aligned sequences in pfamseq (the underlying 
Pfam sequence database) uses to construct the profile HMM for that entry. 
This also contains the more descriptive annotation associated with each entry.

Pfam-A.SARS-CoV-2.full - the aligned sequences in pfamseq that significantly 
match the profile HMM according to the curator defined thresholds.

Pfam-A.SARS-CoV-2.full.uniprot - the aligned sequences in UniProt that 
significantly match the profile HMM according to the curator defined 
thresholds.

The matches.scan and Pfam-A.SARS-CoV-2.hmm have also been updated. 

We have also made individual alignments available for each Pfam entry available, 
which contains both UniProt sequences and the SARS-CoV-2 sequences (which are 
not part of an official UniProt release).  These can be downloaded individually 
from the supplementary_alignments directory or as a compress tarball of all 
alignments (supplementary_alignments.tgz).


Previous Releases:

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.