|
| A Multiple RNA Alignment mode for Stem Loc.
Makes a multiple alignment by progressively aligning new sequences to a seed alignment.
The seed alignment is initially pairwise, and new sequences are added via pairwise comparisons to sequences in the seed.
Thus, all steps involve pairwise sequence-sequence comparisons.
This contrasts to Profile Mode where all the later steps involve profile refinement via sequence-profile comparisons.
Progressive alignment was used e.g. in the CLUSTAL program
(Higgins DG, Sharp PM. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151-3.). |
