[Bioperl-l] {SPECS] Sequence meta data

[Peter Schattner]

Heikki Lehvaslaiho wrote:

> ..When I think about it, I am not quite sure what kind of sequence meta
> information you'd want to store in features... Could you give me
> examples of what you do, please?

What I basically do is define a feature class that inherits from
SeqFeature::Generic.  One of its tags has as its value a reference to what I
call a "Bio::LocatableAnnotationSeq" which is so far identical to a conventional
Bio::LocatableSeq object except that its alphabet error-checking (normally
inherited from PrimarySeq) is over-ridden so that the sequence can contain any
character whatsoever as is appropriate for a "metasequence".   In my
application, the symbols in the metasequence indicate motifs and  RNA
base-pairings of the secondary structure of the sequence (Conventionally one
uses open and closed parentheses to annotate base-pairing.  My encoding is
somewhat more complex and specific to my application, but the idea is the same.)

Pretty simple-mnded but it works for me.  (I use Bio::LocatableSeq, rather than
PrimarySeq,  as my base object because my main use for metasequences is for
annotating SimpleAlign alignments.  I have also had to modify SimpleAlign a
little so it can handle these metasequence objects)

If you want more detailed examples of my code, let me know and I can send you
something off line, but I think this describes all the essentials.

Peter