Stockholm Format - Recommended Features

Recommended Features

#=GF

(See the Pfam and the Rfam documentation under "Description of fields")

Pfam and Rfam may use the following tags:

Compulsory fields: ------------------ AC Accession number: Accession number in form PFxxxxx (Pfam) or RFxxxxx (Rfam). ID Identification: One word name for family. DE Definition: Short description of family. AU Author: Authors of the entry. SE Source of seed: The source suggesting the seed members belong to one family. SS Source of structure: The source (prediction or publication) of the consensus RNA secondary structure used by Rfam. BM Build method: Command line used to generate the model SM Search method: Command line used to perform the search GA Gathering method: Search threshold to build the full alignment. TC Trusted Cutoff: Lowest sequence score (and domain score for Pfam) of match in the full alignment. NC Noise Cutoff: Highest sequence score (and domain score for Pfam) of match not in full alignment. TP Type: Type of family -- presently Family, Domain, Motif or Repeat for Pfam. -- a tree with roots Gene, Intron or Cis-reg for Rfam. SQ Sequence: Number of sequences in alignment. Optional fields: ---------------- DC Database Comment: Comment about database reference. DR Database Reference: Reference to external database. RC Reference Comment: Comment about literature reference. RN Reference Number: Reference Number. RM Reference Medline: Eight digit medline UI number. RT Reference Title: Reference Title. RA Reference Author: Reference Author RL Reference Location: Journal location. PI Previous identifier: Record of all previous ID lines. KW Keywords: Keywords. CC Comment: Comments. NE Pfam accession: Indicates a nested domain. NL Location: Location of nested domains - sequence ID, start and end of insert. WK Wikipedia link: Wikipedia page CL Clan: Clan accession MB Membership: Used for listing Clan membership For embedding trees: ---------------- NH New Hampshire A tree in New Hampshire eXtended format. TN Tree ID A unique identifier for the next tree. Other: ------ FR False discovery Rate: A method used to set the bit score threshold based on the ratio of expected false positives to true positives. Floating point number between 0 and 1.

• Notes: A tree may be stored on multiple #=GF NH lines.
• If multiple trees are stored in the same file, each tree must be preceded by a #=GF TN line with a unique tree identifier. If only one tree is included, the #=GF TN line may be omitted.

#=GS

Rfam and Pfam may use these features:

Feature Description --------------------- ----------- AC ACcession number DE DEscription DR ; ; Database Reference OS Organism (species) OC Organism Classification (clade, etc.) LO Look (Color, etc.)

#=GR

Feature Description Markup letters ------- ----------- -------------- SS Secondary Structure For RNA AaBb...], For protein SA Surface Accessibility (0=0%-10%; ...; 9=90%-100%) TM TransMembrane PP Posterior Probability (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00) LI LIgand binding AS Active Site pAS AS - Pfam predicted sAS AS - from SwissProt IN INtron (in or after) For RNA tertiary interactions: ------------------------------ tWW WC/WC in trans For basepairs: For unpaired: cWH WC/Hoogsteen in cis cWS WC/SugarEdge in cis tWS WC/SugarEdge in trans notes: (1) {c,t}{W,H,S}{W,H,S} for general format. (2) cWW is equivalent to SS.

#=GC

The list of valid features includes those shown below, as well as the same features as for #=GR with "_cons" appended, meaning "consensus". Example: "SS_cons".

Feature Description Description ------- ----------- -------------- RF ReFerence annotation Often the consensus RNA or protein sequence is used as a reference Any non-gap character (e.g. x's) can indicate consensus/conserved/match columns .'s or -'s indicate insert columns ~'s indicate unaligned insertions Upper and lower case can be used to discriminate strong and weakly conserved residues respectively MM Model Mask Indicates which columns in an alignment should be masked, such that the emission probabilities for match states corresponding to those columns will be the background distribution.