Stockholm

http://exon.umdnj.edu/software/RSmatch/Stockholm.html

The "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu.

Example

# STOCKHOLM 1.0
#=GF SQ 21
sp|Q21882|HIUH1_CAEEL -MNKFSLFFALTATL-MTITESAVPTASISAHVLDISGG
#=GS sp|Q21882|HIUH1_CAEEL AC sp|Q21882|HIUH1_CAEEL
#=GS sp|Q21882|HIUH1_CAEEL DE sp|Q21882|HIUH1_CAEEL
sp|O44578|HIUH2_CAEEL -MIKFLLFLAIAAATVISNAELAVPTASISAHVLDISGG
#=GS sp|O44578|HIUH2_CAEEL AC sp|O44578|HIUH2_CAEEL
#=GS sp|O44578|HIUH2_CAEEL DE sp|O44578|HIUH2_CAEEL
sp|O74492|HIUH_SCHPO ----------------MASNPPQPQGPALTAHILNTMSGI
//