Stockholm format is an actively used text data format created in 1997. Stockholm format is a multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors Ralee and Belvu support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate. A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below: # STOCKHOLM 1.0 #=GF ID UPSK #=GF SE Predicted; Infernal #=GF SS Published; PMID 9223489 #=GF RN [1] #=GF RM 9223489 #=GF RT The role of the pseudoknot at the 3' end of turnip yellow mosaic #=GF RT virus RNA in minus-strand synthesis by the viral RNA-dependent RNA #=GF RT polymerase. Read more on Wikipedia...

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  • Stockholm format first appeared in 1997
  • See also: fasta-format
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Example code from Wikipedia:

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.

Last updated August 22nd, 2019