eblume/Tiger-Lily — Issue #21: Support local & global alignment of sequences
Author: eblume
Created: 2011-11-01 16:38:08+00:00
State: open
Labels: feature request

See http://en.wikipedia.org/wiki/Sequence_alignment#Global_and_local_alignments for details on possible algorithms.

At minimum we will need the following new classes:

* AlignedNucleicSequence - a subclass of NucleicSequence which additionally supports '-' (meaning gap). Might also need to support pyramidine vs purine transitions vs transversions - this would also mean supporting the full NCBI FASTA specification.
* AlignedAminoSequence - ditto above.
* LocalSequenceAlignment - query-ably alignment result object, allows printing in standard form as well as metrics
* GlobalSequenceAlignment - ditto. Both probably come from a SequenceAlignment class that does most of the work.
* AlignmentResult - might be needed, unsure - would contain the set of all alignments including relative scores.