Stockholm format

Stockholm format is a multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors Ralee, Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate. Stockholm format files often have the filename extension .sto or .stk. A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below: Stockholm format is a multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors Ralee, Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate. Stockholm format files often have the filename extension .sto or .stk. A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below: Here is a slightly more complex example showing the Pfam CBS domain: A minimal well-formed Stockholm file should contain a header which states the format and version identifier, currently '# STOCKHOLM 1.0', followed by the sequences and corresponding unique sequence names: