Table 12.5.1.

Annotation features found in Rfam Seed alignments

Field name	Field tag	Description
Accession number	AC	Stable accession number for each Rfam family. It is of the form RFxxxxx, where x is a digit.
Identifier	ID	Short and meaningful name for the family. It is not necessarily stable between releases.
Description	DE	A one-line description of the family.
Author	AU	Author of the entry
Seed source	SE	Source of the Seed alignment. May be author, PubMed ID, literature reference, or alignment method.
Secondary structure	SS	Source of the secondary structure mark-up. May be Predicted specifying the software used or Published showing the PubMed ID of the publication where the structure was obtained.
Gathering cutoff	GA	Bit score cutoff chosen to determine whether a match is a real member of the family.
Trusted cutoff	TC	Bit score of the lowest scoring match above the GA threshold.
Noise cutoff	NC	Bit score of the highest scoring match below the GA threshold.
Type	TP	RNA type (controlled vocabulary) must be one of the following:  - Gene   - antisense   - antitoxin   - CRISPR   - microRNA   - lncRNA   - rRNA   - ribozyme   - sRNA   - tRNA   - snRNA    -snoRNA     - CD-box     - HACA-box     - scaRNA    - splicing  - Intron  - Cis-regulatory element   - IRES   - frameshift element   - leader   - riboswitch   - thermoregulator.
Build method	BM	Infernal command line parameters used to construct the family.
Database cross references	DR	GO: Gene Ontology terms SO: Sequence Ontology terms Optional: miRBase identifier, snOPY identifier, database URL, or other cross reference.
Comment	CC	Free text comment.
	WK	Link to a Wikipedia article describing the family.
Sequence count	SQ	Number of sequences in the alignment.
	CL	Rfam clan (if a family is a member of a clan).

The full and up-to-date list is available in the USERMAN file from the Rfam FTP archive (see Internet Resources).