[Blends-commit] r3386 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Mon Jun  4 20:25:55 2012
New Revision: 3386

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3386
Log:
The author Gary Benson <gbenson at bu.edu> wrote at Date: Mon, 04 Jun 2012 16:14:50 -0400:
  Dear Andreas,
  We do not release the source code for TRF.
  Sincerely,
  Gary Benson
So there is no pointin listing it on our TODO list.

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=3386&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Jun  4 20:25:55 2012
@@ -2727,28 +2727,6 @@
  DNA sequence currently will be masked by the program. Sequence comparisons in
  RepeatMasker are performed by one of several popular search engines including,
  cross_match, ABBlast/WUBlast, RMBlast and Decypher.
-
-Depends: trf
-Homepage: http://tandem.bu.edu/trf/trf.html
-License: binary only (non-free)
-Pkg-Description: Tandem Repeats Finder
- A tandem repeat in DNA is two or more adjacent, approximate copies of a
- pattern of nucleotides. Tandem Repeats Finder is a program to locate and
- display tandem repeats in DNA sequences. In order to use the program, the
- user submits a sequence in FASTA format. There is no need to specify the
- pattern, the size of the pattern or any other parameter. The output consists
- of two files: a repeat table file and an alignment file. The repeat table
- contains information about each repeat, including its location, size,
- number of copies and nucleotide content. Clicking on the location indices
- for one of the table entries opens a second web browser that shows an
- alignment of the copies against a consensus pattern. The program is very
- fast, analyzing sequences on the order of .5Mb in just a few seconds.
- Submitted sequences may be of arbitrary length. Repeats with pattern size
- in the range from 1 to 2000 bases are detected. Sequence information sent
- to the server is confidential and deleted after program execution.
-Published-Title: Tandem repeats finder: a program to analyze DNA sequences
-Published-Authors: G. Benson
-Published-In: Nucleic Acids Research
 
 Depends: rmblast
 Homepage: http://tandem.bu.edu/trf/trf.html