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An algorithm for finding tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. TRF uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori knowledge of the pattern, pattern size or number of copies. There are no restrictions on the size of the repeats that can be detected. It uses percentage differences between adjacent copies and treats substitutions and indels separately. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat.

Software type:
Package
Interface:
Graphical user interface
Restrictions to use:
None
Input data:
DNA sequence
Input format:
FASTA
Operating system:
Unix/Linux
Computer skills:
Advanced
Version:
4.09
Stability:
Stable
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Interface:
Web user interface
Restrictions to use:
None
Input data:
DNA sequence
Input format:
FASTA
Computer skills:
Basic
Version:
4.09
Stability:
Stable
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.

Institution(s)

Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY, USA

Funding source(s)

This work was partially supported by NSF grant CCR-9623532.

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    PMID: 9862982
  • (Bergman and Quesneville, 2007) Discovering and detecting transposable elements in genome sequences. Briefings in bioinformatics.
    PMID: 17932080
  • (Anisimova et al., 2015) Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Frontiers in bioengineering and biotechnology.
    PMID: 25853125
  • (Saha et al., 2008) Empirical comparison of ab initio repeat finding programs. Nucleic acids research.
    PMID: 18287116
  • (Lerat, 2010) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity.
    PMID: 19935826
  • (Janicki et al., 2011) Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome research.
    PMID: 21850457

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