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Stockholm format
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Stockholm format
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA 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 well-formed stockholm file always contains a header which states the format and version identifier, currently '# STOCKHOLM 1.0'. The header is then followed by a multiple lines, a mix of markup (starting with #) and sequences. Finally, the "//" line indicates the end of the alignment.
An example without markup looks like:
Sequences are written one per line. The sequence name is written first, and after any number of whitespaces the sequence is written. Sequence names are typically in the form "name/start-end" or just "name". Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".
Mark-up lines start with #. The "parameters" are separated by whitespace, so an underscore ("_") instead of space should be used for the 1-char-per-column markups. Mark-up types defined include:
These feature names are used by Pfam and Rfam for specific types of annotation. (See the Pfam and the Rfam documentation under "Description of fields")
Pfam and Rfam may use the following tags:
Rfam and Pfam may use these features:
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Stockholm format AI simulator
(@Stockholm format_simulator)
Stockholm format
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA 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 well-formed stockholm file always contains a header which states the format and version identifier, currently '# STOCKHOLM 1.0'. The header is then followed by a multiple lines, a mix of markup (starting with #) and sequences. Finally, the "//" line indicates the end of the alignment.
An example without markup looks like:
Sequences are written one per line. The sequence name is written first, and after any number of whitespaces the sequence is written. Sequence names are typically in the form "name/start-end" or just "name". Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".
Mark-up lines start with #. The "parameters" are separated by whitespace, so an underscore ("_") instead of space should be used for the 1-char-per-column markups. Mark-up types defined include:
These feature names are used by Pfam and Rfam for specific types of annotation. (See the Pfam and the Rfam documentation under "Description of fields")
Pfam and Rfam may use the following tags:
Rfam and Pfam may use these features: