Walking tree heuristics for comparative genomic alignments.

Jeffrey D Cavener; Paul Cull; James L Holloway; Tai-Ching Hsu

doi:10.1016/j.mbs.2003.07.001

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Walking tree heuristics for comparative genomic alignments.

Jeffrey D Cavener·Paul Cull·James L Holloway·Tai-Ching Hsu

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Abstract

Genomic sequence data is available for an ever-increasing number of organisms, but the full meaning of this data remains an enigma. String alignment is one approach for deciphering the information contained in genetic strings. Sequences which are conserved across species will help identify genes and other important structures. Similarity between species can be scored by measuring how well their sequences align. The walking tree method is an approximate string alignment method that can handle insertions, deletions, substitutions, translocations, and more than one level of inversion. We will describe this method and recent improvements which allow fast alignment of megabase strings. We will show examples in which the method located or discovered genes. We show how the method can be used to construct phylogenetic trees. We also show that the method can be used to identify essential regions for protein function.

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Animals Computer Graphics Genome Models, Genetic Phylogeny Sequence Alignment Species Specificity Comparative Study Journal Article

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Jeffrey D Cavener, Paul Cull, James L Holloway, Tai-Ching Hsu. Walking tree heuristics for comparative genomic alignments.. https://doi.org/10.1016/j.mbs.2003.07.001

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