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- Title
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
- Authors
Vernikos, Georgios S; Parkhill, Julian
- Abstract
There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.
- Publication
Bioinformatics (Oxford, England), 2006, Vol 22, Issue 18, p2196
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btl369