[Blends-commit] r2765 - /projects/med/trunk/debian-med/tasks/bio

[project2501a-guest at users.alioth.debian.org]

Author: project2501a-guest
Date: Sat Apr 23 19:14:27 2011
New Revision: 2765

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2765
Log:
ADD: Augustus

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2765&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Apr 23 19:14:27 2011
@@ -3738,7 +3738,7 @@
  cross_match, ABBlast/WUBlast, RMBlast and Decypher.
 
 Depends: TRF (Tandem Repeats Finder)
-Homepage: Tandem Repeats Finder
+Homepage: http://tandem.bu.edu/trf/trf.html
 License: binary only (non-free)
  Copyright (C) Dr. Gary Benson 1999-2004. All rights reserved.
  A tandem repeat in DNA is two or more adjacent, approximate copies of a 
@@ -3761,3 +3761,28 @@
  "Tandem repeats finder: a program to analyze DNA sequences"
  Nucleic Acids Research (1999)
  Vol. 27, No. 2, pp. 573-580.
+
+Depends: RMBlast 
+Homepage: http://tandem.bu.edu/trf/trf.html
+License: Same as blast2
+ RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST 
+ suite. The primary difference between this distribution and the NCBI 
+ distribution is the addition of a new program "rmblastn" for use with 
+ RepeatMasker and RepeatModeler. 
+ RMBlast supports RepeatMasker searches by adding a few necessary features 
+ to the stock NCBI blastn program. These include: Support for custom matrices 
+ ( without KA-Statistics ). Support for cross_match-like complexity adjusted 
+ scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. 
+ Support for cross_match-like masklevel filtering.
+
+Depends: Augustus
+Homepage: http://augustus.gobics.de/
+License: not explicitely specified
+ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 
+ It can be run on this web server or be downloaded and run locally. It is 
+ open source so you can compile it for your computing platform. You can now 
+ run AUGUSTUS on the German MediGRID. This enables you to submit larger 
+ sequence files and allows to use protein homology information in the 
+ prediction. The MediGRID requires an instant easy registration by email 
+ for first-time users.
+