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Source: alien-hunter
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
libbiojava-java,
default-jdk
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/alien-hunter/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/alien-hunter/trunk/
Homepage: http://www.sanger.ac.uk/science/tools/alien-hunter
Package: alien-hunter
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
libbytecode-java,
libbiojava-java,
libcommons-cli-java,
libcommons-collections3-java,
libcommons-dbcp-java,
libcommons-pool-java
Suggests: bioperl
Description: Interpolated Variable Order Motifs to identify horizontally acquired DNA
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/.
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