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SALSA: Sequence ALignment via Steiner Ancestors
| Citations: | 3 - 0 self |
BibTeX
@MISC{Lancia_salsa:sequence,
author = {Giuseppe Lancia and R. Ravi},
title = {SALSA: Sequence ALignment via Steiner Ancestors},
year = {}
}
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Abstract
. We describe SALSA (Sequence ALignment via Steiner Ancestors) , a public--domain suite of programs for generating multiple alignments of a set of genomic sequences. We allow the use of either of the two popular objectives, Tree Alignment or Sum-of-Pairs. The main distinguishing feature of our method is that the alignment is obtained via a tree in which the internal nodes (ancestors) are labeled by Steiner sequences for triples of the input sequences. Given lists of candidate labels for the ancestral sequences, we use dynamic programming to choose an optimal labeling under either objective functions. Finally, the fully labeled tree of sequences is turned into into a multiple alignment. Enhancements in our implementation include the traditional space-saving ideas of Hirschberg as well as new data-packing techniques. The running-time bottleneck of computing exact Steiner sequences is handled by a highly effective but much faster heuristic alternative. Finally, other modules ...
Keyphrases
sequence alignment steiner ancestor multiple alignment running-time bottleneck tree alignment ancestral sequence dynamic programming popular objective genomic sequence internal node candidate label optimal labeling steiner sequence traditional space-saving idea input sequence public domain suite heuristic alternative new data-packing technique exact steiner sequence objective function main distinguishing feature
