Stockholm format

Stockholm format
Filename extensions
.sto, .stk
Internet media type
text/x-stockholm-alignment
Developed byErik Sonnhammers
Type of formatBioinformatics
Open format?yes
Websitesonnhammer.sbc.su.se/Stockholm.html

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. Stockholm format files often have the filename extension .sto or .stk.[5]

  1. ^ Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, et al. (January 2009). "Rfam: updates to the RNA families database". Nucleic Acids Research. 37 (Database issue): D136–D140. doi:10.1093/nar/gkn766. PMC 2686503. PMID 18953034.
  2. ^ Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, et al. (January 2008). "The Pfam protein families database". Nucleic Acids Research. 36 (Database issue): D281–D288. doi:10.1093/nar/gkm960. PMC 2238907. PMID 18039703.
  3. ^ Storer J, Hubley R, Rosen J, Wheeler TJ, Smit AF (January 2021). "The Dfam community resource of transposable element families, sequence models, and genome annotations". Mobile DNA. 12 (1): 2. doi:10.1186/s13100-020-00230-y. PMC 7805219. PMID 33436076.
  4. ^ Griffiths-Jones S (January 2005). "RALEE--RNA ALignment editor in Emacs". Bioinformatics. 21 (2): 257–259. doi:10.1093/bioinformatics/bth489. PMID 15377506.
  5. ^ "Alignment Fileformats". 22 May 2019. Retrieved 22 May 2019.