Efficient estimation of pairwise distances between genomes
نویسندگان
چکیده
منابع مشابه
Efficient estimation of pairwise distances between genomes
MOTIVATION Genome comparison is central to contemporary genomics and typically relies on sequence alignment. However, genome-wide alignments are difficult to compute. We have, therefore, recently developed an accurate alignment-free estimator of the number of substitutions per site based on the lengths of exact matches between pairs of sequences. The previous implementation of this measure requ...
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The advent of high throughput sequencers has lead to a dramatic increase in the size of available genomic data. Standard methods, which have worked well for many years, are not suitable for the analysis of big data sets, due to their reliance on a time-consuming alignment step. In this thesis, a new alignment-free approach for phylogeny reconstruction is introduced. The corresponding program, a...
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Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares o...
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MOTIVATION A standard approach to classifying sets of genomes is to calculate their pairwise distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly computing the evolutionary distances between closely related genomes. RESULTS Our distance measure is based on ungapped local alignments that we anchor through pairs of maximal unique matches of a mini...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2009
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btp590