Characterizing the D2 Statistic: Word Matches in Biological Sequences
نویسندگان
چکیده
منابع مشابه
Characterizing the D2 statistic: word matches in biological sequences.
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between two sequences. Recent advances have been made in the characterization of this statistic and in the approximation of its distribution. Here, these results ar...
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Given two sequences over a finite alphabet L, the D2 statistic is the number of m-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we study a generalization of the D2 statistic in the context of DNA sequences, under the assumption of strand symmetric Bernoulli text. For k <m, we look at the count of m-lett...
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Given two sequences over a finite alphabet L, the D2 statistic is the number of m-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we study a generalization of the D2 statistic in the context of DNA sequences, under the assumption of strand symmetric Bernoulli text. For k <m, we look at the count of m-lett...
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Word match counts have traditionally been proposed as an alignment-free measure of similarity for biological sequences. The D(2) statistic, which simply counts the number of exact word matches between two sequences, is a useful test bed for developing rigorous mathematical results, which can then be extended to more biologically useful measures. The distributional properties of the D(2) statist...
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When comparing two sequences, a natural approach is to count the number of k-letter words the two sequences have in common. No positional information is used in the count, but it has the virtue that the comparison time is linear with sequence length. For this reason this statistic D(2) and certain transformations of D(2) are used for EST sequence database searches. In this paper we begin the ri...
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ژورنال
عنوان ژورنال: Statistical Applications in Genetics and Molecular Biology
سال: 2009
ISSN: 1544-6115
DOI: 10.2202/1544-6115.1447