trf
locate and display tandem repeats in DNA sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
trf
About trf
From Debian's package 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, 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.
From Debian's description of the trf package, under that package's license.
Dependencies
Depends on
libc6
Related apps
- wisecomparison of biopolymers, like DNA and protein sequencesCommand line
- prankProbabilistic Alignment Kit for DNA, codon and amino-acid sequencesCommand line
- mapdamagetracking and quantifying damage patterns in ancient DNA sequencesCommand line
- tandem-massmass spectrometry software for protein identificationCommand line
- maqmaps short fixed-length polymorphic DNA sequence reads to reference sequencesCommand line
- fastdnamlTool for construction of phylogenetic trees of DNA sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the trf package, under that package's license.
- Description: Debian's description of the trf package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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