Linked Life Data

20001252

Source:http://linkedlifedata.com/resource/pubmed/id/20001252

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2010-1-5
pubmed:abstractText
Large-scale comparison of the similarities between two biological sequences is a major issue in computational biology; a fast method, the D(2) statistic, relies on the comparison of the k-tuple content for both sequences. Although it has been known for some years that the D(2) statistic is not suitable for this task, as it tends to be dominated by single-sequence noise, to date no suitable adjustments have been proposed. In this article, we suggest two new variants of the D(2) word count statistic, which we call D(2)(S) and D(2)(*). For D(2)(S), which is a self-standardized statistic, we show that the statistic is asymptotically normally distributed, when sequence lengths tend to infinity, and not dominated by the noise in the individual sequences. The second statistic, D(2)(*), outperforms D(2)(S) in terms of power for detecting the relatedness between the two sequences in our examples; but although it is straightforward to simulate from the asymptotic distribution of D(2)(*), we cannot provide a closed form for power calculations.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
1557-8666
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
16
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1615-34
pubmed:dateRevised
2011-9-26
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Alignment-free sequence comparison (I): statistics and power.
pubmed:affiliation
Department of Statistics, University of Oxford, Oxford OX1 3TG, UK.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural