NDLI: Sequence distances based on exhaustive substring composition

Content Provider	IEEE Xplore Digital Library
Author	Apostolico, A. Denas, O.
Copyright Year	2008
Description	Author affiliation: Accademia Naz. dei Lincei & DEI, Univ. of Padova, Padova (Apostolico, A.)
Abstract	The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are hardly fulfilled by the more traditional measures of sequence similarity and distance, like string edit and gene rearrangement, due to a mixture of epistemological and computational problems. Alternative measures, based on the subword composition of sequences, have emerged in recent years and proved to be both fast and effective in a variety of tested cases. The common denominator of such measures is an underlying information theoretic notion of relative compressibility. Their viability depends critically on computational cost. The present paper describes as a paradigm the extension and efficient implementation of one of the methods in this class. The method is based on the comparison of the frequencies of all subwords in the two input sequences, where frequencies are suitably adjusted to take into account the statistical background.
Starting Page	95
Ending Page	98
File Size	364953
Page Count	4
File Format	PDF
ISBN	9781424422692
e-ISBN	9781424422715
DOI	10.1109/ITW.2008.4578629
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-05-05
Publisher Place	Portugal
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences Genomics Drives Biology computing Frequency Educational institutions Organisms Phylogeny Computational efficiency Bioinformatics
Content Type	Text
Resource Type	Article

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