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Statistical considerations underpinning an alignment-free sequence comparison method

Jing, Junmei; Burden, Conrad; Foret, Sylvain; Wilson, Susan

Description

The D2 statistic is defined as the number of word matches of prespecified length k, with up to t mismatches, shared between two given sequences. This statistic finds its application in alignment-free comparisons of biological sequences. It has two main advantages over alignment-based methods for nucleotide and amino-acid sequence comparisons, such as BLAST (basic local alignment search tool). These are (i) D2 does not assume that homologous segments are contiguous, and (ii) the algorithm is...[Show more]

CollectionsANU Research Publications
Date published: 2010
Type: Journal article
URI: http://hdl.handle.net/1885/37507
Source: Journal of the Korean statistical society
DOI: 10.1016/j.jkss.2010.02.009

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