Stockholm format is a text data format created in 1997.
| #2886on PLDB | 27Years Old |
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...
Feature Description Description
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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.