Efficient estimation of pairwise distances between genomes | Zendy

Mirjana Domazet-Lošo | Zendy; Bernhard Haubold | Zendy

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Efficient estimation of pairwise distances between genomes

Author(s) -

Mirjana Domazet-Lošo,

Bernhard Haubold

Publication year - 2009

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btp590

Subject(s) - genome , computer science , pairwise comparison , tree traversal , tree (set theory) , suffix tree , sequence (biology) , source code , algorithm , combinatorics , data structure , biology , mathematics , genetics , artificial intelligence , gene , programming language , operating system

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 requires n(n-1) suffix tree constructions and traversals, where n is the number of sequences analyzed. This does not scale well for large n.

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