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---++ StockholmFormat

StockholmFormat is a flatfile format for databases of annotated multiple sequence alignments.

It is the format used e.g. by
the [[http://www.sanger.ac.uk/Software/Pfam/][Pfam]]
and [[http://www.sanger.ac.uk/Software/Rfam/][Rfam]]
databases, containing alignments of protein and RNA families,
respectively.

[[http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html][Erik Sonnhammer's group's page]] has the format spec
(AlexCoventry - 28 Feb 2005).

Here is [[%YAMURLPATH%/Stockholm.html][our mirror]] of that page (IanHolmes).

Stockholm now has a wikipedia page:
   * Wikipedia:Stockholm_format

Stockholm shows by-column alignment annotations, such as RNA secondary structure, in a compact
and (if appropriately indented) human-readable way.
For example (pairwise alignment of purine riboswitches):

<pre>
# STOCKHOLM 1.0
#=GC SS_cons       .................<<<<<<<<...<<<<<<<........>>>>>>>..
AP001509.1         UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU
#=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..--
AE007476.1         AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU
#=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----

#=GC SS_cons       ......<<<<<<<.......>>>>>>>..>>>>>>>>...............
AP001509.1         CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
#=GR AP001509.1 SS -------<<<<<--------->>>>>--->>>>>>>>---------------
AE007476.1         UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
#=GR AE007476.1 SS ------.<<<<<--------->>>>>.-->>>>>>>>---------------
//
</pre>

Stockholm allows sequences to be split over multiple lines (as in the above example),
though this is "discouraged" in the spec.

---++ StockholmTools

See StockholmTools for a list of tools for working with StockholmFormat.

Also see the [[http://doc.bioperl.org/releases/bioperl-1.4/Bio/AlignIO/stockholm.html][Bioperl Stockholm class]].

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