Stockholm format is a flatfile format for databases of annotated multiple sequence alignments. It is used by the Pfam (for protein family alignments) and Rfam (for RNA family alignments) databases.
Stockholm shows by-column alignment annotations, such as RNA secondary structure, in a compact and (if appropriately indented) human-readable way. It allows sequences to be split over multiple lines, although this is “discouraged” in the specification.
BioPerl currently supports reading single-line, multi-line, and interleaved Stockholm formats. Planned Stockholm alignment output using write_aln() will only support single-line and interleaved formats (i.e. similar to Pfam and Rfam output). Currently only Pfam-like single-line output is implemented.
# 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 ------.<<<<<--------->>>>>.-->>>>>>>>---------------
//