[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

Chris Fields cjfields at uiuc.edu
Fri Oct 27 18:34:57 UTC 2006

I am working an refactoring the AlignIO::stockholm parser to get it reading
and writing Pfam/Rfam alignments, and noticed that many alignments have
EMBL-like annotations attached, which pertain to the entire alignment:

#=GF ID    ykkC-yxkD
#=GF AC    RF00442
#=GF DE    ykkC-yxkD element
#=GF AU    Moxon SJ
#=GF GA    20.0
#=GF NC    0.1
#=GF TC    59.4
#=GF SE    Barrick JE, Breaker RR
#=GF SS    Predicted; Barrick JE, Breaker RR
#=GF TP    Cis-reg; riboswitch;
#=GF BM    cmbuild CM SEED
#=GF BM    cmsearch -W 175 CM SEQDB
#=GF RN    [1]
#=GF RM    15096624
#=GF RT    New RNA motifs suggest an expanded scope for riboswitches in
#=GF RT    bacterial genetic control.
#=GF RA    Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J,
#=GF RA    M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR;
#=GF RL    Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF CC    This family represents the bacterial ykkC/yxkD element. The
function of
#=GF CC    this family is unclear although it has been suggested that it may
#=GF CC    to switch on efflux pumps and detoxification systems in response
to harmful
#=GF CC    environmental molecules [1]. The Thermoanaerobacter tengcongensis
#=GF CC    EMBL:AE013027 overlaps with Rfam:RF00167 suggesting that the two
#=GF CC    riboswitches may work in conjunction to regulate the the upstream
#=GF CC    which codes for Swiss:Q8RC62, a member of Pfam:PF00860 (Personal
obs. Moxon
#=GF CC    SJ).
#=GF SQ    16

SimpleAlign, as implemented, seemingly doesn't have a way to store this

I'll work on getting the core alignment IO working, but would there be any
interest in having a way to store annotations in Bio::SimpleAlign?  I'm
guessing the methods would be similar to the various Bio::Seq Annotation


Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

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