Tandem repeat detection software tools | Genome annotation
Tandem repeats (TRs) represent one of the most prevalent features of genomic sequences. Due to their abundance and functional significance, a plethora of detection tools has been devised over the last two decades.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Detects tandem repeats in DNA sequences without needing pattern or pattern size. TRF exploits a probabilistic model of tandem repeats and several statistical criteria based on that model. It uses also an algorithm of k-tuple matching to avoid full scale alignment matrix computations. This software has detection and analysis components: the detection part finds candidate tandem repeats and the analysis part deals with generating an alignment for each candidate with statistics and nucleotide sequence.
Detects several types of repeats and provides an evaluation of significance as well as interactive visualization. REPuter was designed to be used in studies of repetitive DNA on a genomic or inter-genomic scale. The software enables the comparison of two or more sequences by concatenating them, and then searching for repeats. It utilizes the search engine REPfind which uses an implementation of suffix trees to locate exact repeats in linear space and time.
Solves eﬃciently large scale sequence matching tasks. Vmatch is a versatile software that can process sequences over any user defined alphabet not larger than 250 symbols. This method fully implements the concept of symbol mappings, denoting alphabet transformations. Vmatch subsumes the software tool REPuter but is much more general, with a very flexible user interface, and improved space and time requirement.
A user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. SciRoKo contains two main modules: a simple sequence repeat (SSR) search module, which supports five different SSR search modes and a module for SSR-statistics, notably for mismatch frequency and compound microsatellite analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites.
An approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. PILER is a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster.
Allows identification of tandemly repeated structures in DNA sequences. mreps is constituted by an exhaustive combinatorial algorithms used to find all repeats verifying certain mathematical properties. The software can be used for locating a particular type of tandem repeat, or to make a fast genome-wide analysis of tandemly repeated patterns. It is also able to identify loose repeats through a special resolution parameter.