[Cdd-commits] r995 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Jul 22 09:58:39 2008
New Revision: 995

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added ACT


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Jul 22 09:58:39 2008
@@ -1690,20 +1690,40 @@
 Homepage: http://www.sanger.ac.uk/Software/analysis/alien_hunter/
 License: GPL
 Pkg-Description: Interpolated Variable Order Motifs for identification of 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
+ 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
+ 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
 Comment: The archive contains biojava 1.4 - but we should focus on
  Debian packaged BioJava.
+
+Depends: act
+Homepage: http://www.sanger.ac.uk/Software/ACT/
+License: GPL
+Pkg-Description: DNA Sequence Comparison Viewer
+ ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer
+ based on Artemis. In common with Artemis, ACT is written in Java and
+ runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can
+ read complete EMBL and GENBANK entries or sequence in FASTA or raw
+ format. Extra sequence features can be in EMBL, GENBANK or GFF
+ format.
+ .
+ The sequence comparison displayed by ACT is usually the result of
+ running a blastn or tblastx search. See the user manual for more
+ information.
+ .
+ To see ACT in action go to the examples page
+ http://www.sanger.ac.uk/Software/ACT/Examples/