[Blends-commit] r2764 - /projects/med/trunk/debian-med/tasks/bio

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

Author: project2501a-guest
Date: Sat Apr 23 18:50:00 2011
New Revision: 2764

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2764
Log:
ADD: TRF (Tandem Repeats Finder)

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=2764&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Apr 23 18:50:00 2011
@@ -3736,3 +3736,28 @@
  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 (Tandem Repeats Finder)
+Homepage: Tandem Repeats Finder
+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 
+ 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.
+
+ Please cite:
+ G. Benson,
+ "Tandem repeats finder: a program to analyze DNA sequences"
+ Nucleic Acids Research (1999)
+ Vol. 27, No. 2, pp. 573-580.