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[ Källkod: alien-hunter  ]

Paket: alien-hunter (1.7-1) [universe]

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Please consider filing a bug or asking a question via Launchpad before contacting the maintainer directly.

Original Maintainers (usually from Debian):

  • Debian Med Packaging Team (E-postarkiv)
  • Andreas Tille

It should generally not be necessary for users to contact the original maintainer.

Externa resurser:

Liknande paket:

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/.

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

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