Pfam annotation of ORFs
======

Pfam is a database of protein families.

 - Website: https://pfam.xfam.org/

 - Citation: Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA,
   Sonnhammer EL, Tosatto SC, Paladin L, Raj S, Richardson LJ, Finn RD. Pfam:
   The protein families database in 2021. Nucleic acids research. 2021 Jan 8;
   49(D1):D412-9.

Pfam release 35.0 (2021-11) was used to annotate the ORFs. Specifically, the
HMM-based mapping (i.e., Pfam-A.hmm) was used.

 - Source: http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/

PfamScan v1.6 was used to perform the annotation. Command:

```
pfam_scan.pl -cpu # -fasta input.faa -dir db > output.tblout
```

Statistics:

 - Total number of matches: 54,185,026
 - Number of annotated ORFs: 35,888,191
 - Number of unique Pfams: 13,574

Database files:

 - orf-to-pfam.map: Mapping of ORF to Pfams. There may be multiple Pfams,
   sorted by their locations in the ORF. Some Pfams may occur multiple times
   in an ORF.

 - orf-to-pfam_uniq.map: Mapping of ORF to Pfams, excluding duplicate Pfams
   (i.e., same repeat occurs only once). Note: There could still be multiple
   unique Pfams mapped to one ORF.

 - pfam_name.txt: Names of Pfams.

 - pfam_description.txt: Descriptions of Pfams.

 - pfam_type.txt: Types of Pfams. There are six types:

   - Family (n=7,788), Domain (5,155), Repeat (451), Coiled-coil (110), Motif
     (55), Disordered (15).

 - pfam-to-clan.map: Mapping of Pfams to names, which are higher-order groups.
   This mapping is unique.

 - clan_name.txt: Names of clans.

 - clan_description.txt: Descriptions of clans.

 - pfam-to-interpro.map: Mapping of Pfams to InterPro entries.

 - pfam-to-go/: Mappings of Pfams to Gene Ontology (GO) terms.

Additional files:

 - pfamscan.tsv: PfamScan output file, converted from HMMER tblout into TSV
   format, excluding header. Columns:

   - <seq id> <alignment start> <alignment end> <envelope start> <envelope end>
     <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score>
     <E-value> <significance> <clan>

Collapsing order:

```
  ORF > Pfam > Clan
         v      v
        name   name
```