Difference between revisions of "TRF"
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Revision as of 16:33, 10 August 2012
Description
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.
Execution Environment and Modules
To use trf with the environment modules system at HPC the following commands are available:
Get module information for trf:
$module spider trf
Load the default application module:
$module load trf
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_TRF_DIR - directory where trf is located.
Citation
If you publish research that uses trf you have to cite it as follows: G. Benson, "Tandem repeats finder: a program to analyze DNA sequences", Nucleic Acids Research (1999), Vol. 27, No. 2, pp. 573-580.