RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Computational identification of evolutionarily conserved exons
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
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High-throughput DNA sequencing is now producing collections of genomes from moderately or closely related organisms. Such a collection may be represented as a multiple alignment M of orthologous sequences, which induces a phylogenetic tree τ. Long-range genomic alignments with phylogenies have not yet found a prominent place in BLAST-like similarity search algorithms, though using them directly as databases can potentially yield more accurate and more informative alignments. This work describes how to construct local alignments between a query and a multiple alignment in a way that explicitly uses a phylogenetic tree τ. We give an EM algorithm to find a locally optimal alignment when the location of the query on the tree τ is not known. An initial implementation of the method is tested on a large multiple alignment of sequences from eight vertebrate genomes.