[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

[Hilmar Lapp]

You could make SimpleAlign be a Bio::AnnotationHolderI. (I suppose  
this is what you meant by the 'various Bio::Seq Annotation methods'  
too.)

Just to make sure I'm not misunderstanding, I suppose the annotation  
pertains to the entire alignment?

	-hilmar

On Oct 27, 2006, at 2:34 PM, Chris Fields wrote:

> 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:
>
> # STOCKHOLM 1.0
> #=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,
> Lee
> #=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
> function
> #=GF CC    to switch on efflux pumps and detoxification systems in  
> response
> to harmful
> #=GF CC    environmental molecules [1]. The Thermoanaerobacter  
> tengcongensis
> sequence
> #=GF CC    EMBL:AE013027 overlaps with Rfam:RF00167 suggesting that  
> the two
> #=GF CC    riboswitches may work in conjunction to regulate the the  
> upstream
> gene
> #=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
> information.
>
> 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
> methods.
>
> Chris
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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