[BioRuby] Alignment plugin

Rutger Vos rutgeraldo at gmail.com
Mon Apr 26 15:40:11 UTC 2010

On Mon, Apr 26, 2010 at 4:04 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Maybe we should start defining a basic sequence object. What would we
> want from it, what should be core and what should be mixed in?
> Alignments and secondary structures should build on that.

In the interest of learning from other Bio* projects ;-) it should be
noted that there is a bit of a mismatch between sequences as
standalone objects on the one hand, and rows within character state
matrices on the other, especially when you consider types of data
beyond molecular sequences (e.g. morphological character state data).
Within a matrix there are columns such that every cell in a sequence
now becomes a concrete instance of one of a limited set of character
states for that character/column. Especially for morphological data
there could be very esoteric ambiguity mappings from one state in that
column to another. Imagine an alignment with unique mappings a la the
IUPAC single character codings for each column. The upshot might be
that you'd need a mapping object for each cell, though you'd use an
immutable class for molecular data.

Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
United Kingdom
Tel: +44 (0) 118 378 7535

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