Tandem repeats finder: a program to analyze DNA sequences

Nucleic Acids Res. 1999 Jan 15;27(2):573-80. doi: 10.1093/nar/27.2.573.

Abstract

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Chromosomes, Fungal / genetics
  • Cluster Analysis
  • Friedreich Ataxia / genetics
  • Genes, Fungal
  • Humans
  • Iron-Binding Proteins*
  • Mannose-Binding Lectins
  • Membrane Proteins
  • Models, Statistical
  • Mutation
  • Pattern Recognition, Automated*
  • Phosphotransferases (Alcohol Group Acceptor) / genetics
  • Probability
  • Pseudogenes
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Saccharomyces cerevisiae Proteins*
  • Sequence Analysis, DNA / methods*
  • Software
  • Tandem Repeat Sequences*

Substances

  • FLO1 protein, S cerevisiae
  • Iron-Binding Proteins
  • Mannose-Binding Lectins
  • Membrane Proteins
  • Receptors, Antigen, T-Cell, alpha-beta
  • Saccharomyces cerevisiae Proteins
  • frataxin
  • Phosphotransferases (Alcohol Group Acceptor)