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OMIC
08608

Tandem Repeat Annotation Library TRAL

Makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
Python
Computer skills:
Advanced
Version:
TRAL version 0.3
Stability:
Stable
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Documentation & support

Maintainer

  • Elke Schaper <elke.schaper at isb-sib.ch>

Credits

Institution(s)

SIB Swiss Institute of Bioinformatics, Quartier Sorge 1015 Lausanne

Publications

  • (Schaper et al., 2015) TRAL: Tandem repeat annotation library. Bioinformatics.
    PMID: 25987568

Classification

Literature

  • (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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