kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison
نویسندگان
چکیده
منابع مشابه
kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison
MOTIVATION Alignment-based methods for sequence analysis have various limitations if large datasets are to be analysed. Therefore, alignment-free approaches have become popular in recent years. One of the best known alignment-free methods is the average common substring approach that defines a distance measure on sequences based on the average length of longest common words between them. Herein...
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The vast majority of sequence comparison methods for phylogeny reconstruction rely on pairwise or multiple sequence alignments. These approaches are in practice not usable for longer sequences such as complete genomes. For this reason alignment-free methods have recently become more popular because they are much faster and usually computable in linear time. Some of these methods are based on re...
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We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our method is a new measure of pairwise distances between sequences. This measure is based on computing the average lengths of maximum common substrings, which is intrinsically related to information theoretic tools (Kullbac...
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In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free methods rely on exact word matches to estimate pairwise similarities or distances between the input sequences. By contrast, our new algorithms are based on inexact word matches. The first of these approaches uses the relative frequencies of...
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The “Common Substring Alignment” problem is defined as follows. The input consists of a set of strings S1, S2 . . . , Sc , with a common substring appearing at least once in each of them, and a target string T . The goal is to compute similarity of all strings Si with T , without computing the part of the common substring over and over again. In this paper we consider the Common Substring Align...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btu331