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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 )
and (Belvu ) support Stockholm format as do the probabilistic database search tools, (Infernal ) and HMMER, and the phylogenetic analysis tool Xrate. A simple example of an Rfam alignment (UPSK RNA) with a pseudoknot in Stockholm format is shown below:
# STOCKHOLM 1.0
#=GF ID UPSK
#=GF SE Predicted; Infernal
#=GF SS Published; PMID 9223489
#=GF RN ()
#=GF RM 9223489
#=GF RT The role of the pseudoknot at the 3' end of turnip yellow mosaic
#=GF RT virus RNA in minus-strand synthesis by the viral RNA-dependent RNA
#=GF RT polymerase.
#=GF RA Deiman BA, Kortlever RM, Pleij CW;
#=GF RL J Virol 1997;71:5990-5996.
AF035635.1/619-641 UGAGUUCUCGAUCUCUAAAAUCG
M24804.1/82-104 UGAGUUCUCUAUCUCUAAAAUCG
J04373.1/6212-6234 UAAGUUCUCGAUCUUUAAAAUCG
M24803.1/1-23 UAAGUUCUCGAUCUCUAAAAUCG
#=GC SS_cons .AAA....<<<>>>
//
Here is a slightly more complex example showing the Pfam CBS domain:
# STOCKHOLM 1.0
#=GF ID CBS
#=GF AC PF00571
#=GF DE CBS domain
#=GF AU Bateman A
#=GF CC CBS domains are small intracellular modules mostly found
#=GF CC in 2 or four copies within a protein.
#=GF SQ 5
#=GS O31698/18-71 AC O31698
#=GS O83071/192-246 AC O83071
#=GS O83071/259-312 AC O83071
#=GS O31698/88-139 AC O31698
#=GS O31698/88-139 OS Bacillus subtilis
O83071/192-246 MTCRAQLIAVPRASSLAEAIACAQKMRVSRVPVYERS
#=GR O83071/192-246 SA 9998877564535242525515252536463774777
O83071/259-312 MQHVSAPVFVFECTRLAYVQHKLRAHSRAVAIVLDEY
#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEE
O31698/18-71 MIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPS
#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHHEEEEEEEEEEEEEEEEHHH
O31698/88-139 EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHHHEEEEEEEEEEEEEEEEEH
#=GC SS_cons CCCCCHHHHHHHHHHHHHEEEEEEEEEEEEEEEEEEH
O31699/88-139 EVMLTDIPRLHINDPIMKGFGMVINN..GFVCVENDE
#=GR O31699/88-139 AS ________________
*____________________
#=GR O31699/88-139 IN ____________1____________2______0____
//
A minimal well formed Stockholm files should contain the header which states the format and version identifier, currently '# STOCKHOLM 1.0'. Followed by the sequences and corresponding unique sequence names:
'' stands for "sequence name", typically in the form "name/start-end" or just "name". Finally, the "//" line indicates the end of the alignment. Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".
==The alignment mark-up==
Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.
#=GF
#=GC
#=GS
#=GR
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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