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alien-hunter: Interpolated Variable Order Motifs to identify horizontally acquired DNA

Distribution Debian testing
Abteilung science
Quelle alien-hunter
Version 1.7-1
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Beschreibung Alien_hunter is an application for the prediction of putative
Horizontal Gene Transfer (HGT) events with the implementation of
Interpolated Variable Order Motifs (IVOMs). An IVOM approach
exploits compositional biases using variable order motif distributions
and captures more reliably the local composition of a sequence compared
to fixed-order methods. Optionally the predictions can be parsed into a
2-state 2nd order Hidden Markov Model (HMM), in a change-point detection
framework, to optimize the localization of the boundaries of the
predicted regions. The predictions (embl format) can be automatically
loaded into Artemis genome viewer freely available at:
http://www.sanger.ac.uk/Software/Artemis/.
.
The manuscript describing the alien_hunter algorithm is available
from Bioinformatics: Interpolated variable order motifs for
identification of horizontally acquired DNA: revisiting the
Salmonella pathogenicity islands. Vernikos GS, Parkhill J
Bioinformatics. 2006;. PMID: 16837528
Abhängig vonlibbiojava-java, libbytecode-java, libcommons-cli-java, libcommons-collections-java, libcommons-dbcp-java, libcommons-pool-java
Vorgeschlagenbioperl
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