[Debian-med-packaging] Bug#963950: ITP: trf -- locate and display tandem repeats in DNA sequences
Andreas Tille
tille at debian.org
Mon Jun 29 07:05:03 BST 2020
Package: wnpp
Severity: wishlist
Subject: ITP: trf -- locate and display tandem repeats in DNA sequences
Package: wnpp
Owner: Andreas Tille <tille at debian.org>
Severity: wishlist
* Package name : trf
Version : 4.09.1
Upstream Author : Gary Benson <gbenson at bu.edu>,
* URL : https://tandem.bu.edu/trf/trf.html
* License : AGPL-3+
Programming Lang: C
Description : locate and display tandem repeats in DNA sequences
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, viewable in a web browser, 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 browser page 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.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/trf
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