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 codice_1 or codice_2. Syntax. A well-formed stockholm file always contains a header which states the format and version identifier, currently ". 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: Recommended features. These feature names are used by Pfam and  Rfam for specific types of annotation. Section::::#=GF. Pfam and Rfam may use the following tags: Section::::#=GS. Rfam and Pfam may use these features: Section::::#=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". Size limits. There are no explicit size limits on any field. However, a simple parser that uses fixed field sizes should work safely on Pfam and Rfam alignments with these limits: Examples. 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: