Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments.
[1][2][3] The alignment editors Ralee,[4] Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate.
The header is then followed by a multiple lines, a mix of markup (starting with #) and sequences.
The "parameters" are separated by whitespace, so an underscore ("_") instead of space should be used for the 1-char-per-column markups.
However, a simple parser that uses fixed field sizes should work safely on Pfam and Rfam alignments with these limits: A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below:[6] Here is a slightly more complex example showing the Pfam CBS domain: