Transposable element detection software tools | Genome annotation
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks—that is, no standard way to measure or compare their accuracy.
Screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program.
A software tool which screens query sequences against a reference collection of repeats and "censors" (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.
Allows de novo identification and modelling. RepeatModeler is composed of two programmes, RECON and RepeatScout, based on complementary computational methods. It is able to recognise repeat element boundaries and family relationships from sequence data. The tool automates the runs of RECON and RepeatScout given a genomic database and employs the returned information to build, refine and classify consensus models of putative interspersed repeats.
A package to discover repetitive substrings in DNA. RepeatScout identifies repeat family sequences from genomes where hand-curated repeat databases are not available. The output of this program can be used as input to RepeatMasker as a way of automatically masking newly-sequenced genomes. It includes more or less 3 Mb of the human X chromosome for testing and debugging purposes.
A platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. RetroTector online (ROL) is a reduced, web-based version of RetroTector. ROL provides 1. annotation and presentation of known retroviral sequences, 2. detection of proviral chains in unknown genomic sequences, with up to 100 Mbase per submission.
Given DNA sequences, it predicts locations and structure of full-length LTR retrotransposons accurately by considering common structural features. LTR_FINDER is a system capable of scanning large-scale sequences rapidly and the first web server for ab initio LTR retrotransposon finding.
An efficient software tool delivering high quality annotation of LTR retrotransposons. LTRharvest can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes LTRharvest a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.