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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…
RepeatScout
Desktop

RepeatScout

A package to discover repetitive substrings in DNA. RepeatScout identifies…

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…

P-clouds
Desktop

P-clouds

Identifies repeat structures in large eukaryotic genomes using oligonucleotide…

Identifies repeat structures in large eukaryotic genomes using oligonucleotide counts. P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that…

RepeatFinder
Desktop

RepeatFinder

Identifies repeats in genomes for both complete and partial sequences.…

Identifies repeats in genomes for both complete and partial sequences. RepeatFinder detects repeats information by using a comprehensive set of exact repeats as a basis and assign them in similarity…

RTAnalyzer
Web

RTAnalyzer

Searches retro-transposition elements in the human genome. RTAnalyzer is a web…

Searches retro-transposition elements in the human genome. RTAnalyzer is a web application which allows to find retrotransposons and analyze for the presence of the L1 signature. The software is…

MITE-Hunter
Desktop

MITE-Hunter

A program pipeline that can identify MITEs as well as other small Class 2…

A program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets.

MGEScan
Desktop
Web

MGEScan

MGEScan-LTR and MGEScan-nonLTR are successfully used programs for identifying…

MGEScan-LTR and MGEScan-nonLTR are successfully used programs for identifying long terminal repeats (LTR) and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not…

TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

SINE_scan
Desktop

SINE_scan

Predicts short interspersed nuclear elements (SINE) elements in genomic DNA…

Predicts short interspersed nuclear elements (SINE) elements in genomic DNA sequences. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in…

phRAIDER
Desktop

phRAIDER pattern-hunter based Rapid Ab Initio Detection of Elementary Repeats

A software tool for the de novo identification of genome repeat elements that…

A software tool for the de novo identification of genome repeat elements that is applicable to assembled genomes. The underlying model is a new definition of elementary repeats that incorporates the…

LTRtype
Desktop

LTRtype

Mines increasingly sequenced genomes by using multithreading technologies.…

Mines increasingly sequenced genomes by using multithreading technologies. LTRtype is a software program to identify different types of structurally complex long terminal repeat (LTR)…

TASR
Desktop

TASR Transposon Annotation using Small RNAs

De novo annotation of transposable elements (TEs) in Arabidopsis, rice and…

De novo annotation of transposable elements (TEs) in Arabidopsis, rice and soybean. The use of TASR pipeline for TE annotation in plants will lead to a better understanding of the biological and…

PASTEC
Desktop

PASTEC

Classifies transposable elements (TEs) by searching for structural features and…

Classifies transposable elements (TEs) by searching for structural features and similarities. PASTEC, developed in the REPET package, allows to classify TEs automatically to order level, for all nine…

EnHERV
Web

EnHERV Human Endogenous Retrovirus Enrichment Tool

Provides the identified endogenous retrovirus repetitive sequences from Repbase…

Provides the identified endogenous retrovirus repetitive sequences from Repbase Update that are present in the human genome. EnHERV offers an enrichment analysis function that allows users to perform…

ReTe
Web
Desktop

ReTe RetroTector

A platform-independent Java program for identification and characterization of…

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…

retrotransposon…
Desktop

retrotransposons-spread

Studies the propagation of long terminal repeat (LTR) retrotransposons inside…

Studies the propagation of long terminal repeat (LTR) retrotransposons inside eukaryotic genomes. The model retrotransposons-spread allows us to take into account both the positions and the…

CLARI-TE
Desktop

CLARI-TE

Predicts Transposable Elements (TEs) in complexe genome such as wheat. CLARI-TE…

Predicts Transposable Elements (TEs) in complexe genome such as wheat. CLARI-TE corrects raw similarity search result from RepeatMasker. It automated two processes: (i) correction of the…

Genome ARTIST
Desktop

Genome ARTIST Genome ARtificial Transposon Insertion Site Tracker

A bioinformatics tool originally developed in order to allow a rapid detection…

A bioinformatics tool originally developed in order to allow a rapid detection of insertional mutations generated in the genome of Drosophila melanogaster by means of artificial P element…

LTR_retriever
Desktop

LTR_retriever

Removes false positives from initial software predictions. LTR retriever is a…

Removes false positives from initial software predictions. LTR retriever is a software for identification of long terminal repeat retrotransposons (LTR-RTs). It achieves very high specificity,…

REannotate
Desktop

REannotate Repetitive Element re-annotation

Processes REPEAT MASKER annotation for automated i) defragmentation of…

Processes REPEAT MASKER annotation for automated i) defragmentation of dispersed repetitive elements, ii) resolution of the temporal order of insertions in clusters of nested elements, and iii)…

InFiRe
Desktop
Web

InFiRe Insertion Finder via Restriction digest

Allows for the computational identification of transposon insertion sites in…

Allows for the computational identification of transposon insertion sites in known bacterial genome sequences after transposon mutagenesis experiments. The used approach is based on the observation…

Red
Desktop

Red

A repeat-detection tool capable of labeling its training data and training…

A repeat-detection tool capable of labeling its training data and training itself automatically on an entire genome. Red is easy to install and use. It is sensitive to both transposons and simple…

MITE Digger
Desktop

MITE Digger

A software for the de novo retrieval of miniature inverted repeat transposable…

A software for the de novo retrieval of miniature inverted repeat transposable elements (MITEs) at genomic scales with high accuracy, specificity and efficiency. MITE digger was developed to increase…

VisualTE
Desktop

VisualTE

A JAVA stand-alone graphical interface that allows users to visualize and…

A JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable…

DAWGPAWS
Desktop

DAWGPAWS

A tool for discovering the location of the genes and transposable elements in…

A tool for discovering the location of the genes and transposable elements in eukaryotic genomic sequences. DAWGPAWS is distributed as a suite of command line programs that are designed to assist a…

Transpogene
Dataset

Transpogene

A database of Transposed elements (TEs) which are located within protein-coding…

A database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. TranspoGene contains…

LTRdigest
Desktop

LTRdigest

A software tool for automated annotation of internal features of putative LTR…

A software tool for automated annotation of internal features of putative LTR retrotransposons. LTRdigest uses local alignment and hidden Markov model-based algorithms to detect…

PLOTREP
Web

PLOTREP

It is designed to be used by anyone who would like to identify interspersed…

It is designed to be used by anyone who would like to identify interspersed repetitive elements in BAC-sized or smaller genomic regions. PLOTREP can merge fragments belonging to the same copy of a…

LTR_Finder
Web

LTR_Finder

Given DNA sequences, it predicts locations and structure of full-length LTR…

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…

GREAM
Desktop
Web

GREAM Genomic Repeat Element Analyzer for Mammals

A web-server for analysis, screening and selection of potentially important…

A web-server for analysis, screening and selection of potentially important mammalian genomic repeats. GREAM has been developed to identify over-/under-represented elements in, a) the promoters or…

LTRclassifier
Web

LTRclassifier

Classifies plant long terminal repeat (LTR) retrotransposons in their…

Classifies plant long terminal repeat (LTR) retrotransposons in their respective superfamily, and provides automatically a basic functional annotation of these elements. LTRclassifier was tested on…

detectMITE
Desktop

detectMITE

A MATLAB-based program that employs a novel numeric calculation algorithm to…

A MATLAB-based program that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in miniature inverted repeat transposable elements (MITE) detection in…

REMiner
Desktop

REMiner

Surveys and characterizes the chromosome wide occurrence, distribution, and…

Surveys and characterizes the chromosome wide occurrence, distribution, and arrangement configuration of repetitive elements (REs) for the individual human chromosomes. REMiner consists of two main…

LTR Annotator
Desktop

LTR Annotator

Combines de novo long terminal repeat (LTR) detection and LTR annotation…

Combines de novo long terminal repeat (LTR) detection and LTR annotation together with removal of potential false-positive LTRs. LTR Annotator is a pipeline that delivers detailed results of LTR…

MASiVE
Desktop
Web

MASiVE Mapping and Analysis of Sirevirus Elements

An expertly built tool for the large-scale, yet sensitive and highly accurate,…

An expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic…

LTR_STRUC
Desktop

LTR_STRUC LTR retrotransposon structure program

Identifies and automatically analyzes LTR retrotransposons in genome databases…

Identifies and automatically analyzes LTR retrotransposons in genome databases by searching for structural features characteristic of such elements. LTR_STRUC has significant advantages over…

HomologMiner
Desktop

HomologMiner

Identifies homologous groups applicable to genome sequences that have been…

Identifies homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats. HomologMiner incorporates several new…

iMapper
Web

iMapper Insertional Mutagenesis Mapper

A web application for the efficient analysis of insertion site sequence reads…

A web application for the efficient analysis of insertion site sequence reads against vertebrate and invertebrate Ensembl genomes. Taking linker based sequences as input, iMapper scans and trims the…

Greedier
Desktop

Greedier

An iterative algorithm to find repeats in a target genome given a repeat…

An iterative algorithm to find repeats in a target genome given a repeat library. Greedier distinguishes itself from existing methods by taking into account the fragmentation of repeats. Each…

DomainOrganizer
Web

DomainOrganizer

Proposes a synthetic view of a set of DNA sequences by providing both a…

Proposes a synthetic view of a set of DNA sequences by providing both a segmentation of them into domains and a classification on the basis of these domains. DomainOrganizer aligns the sequences,…

MaskerAid
Desktop

MaskerAid

A software enhancement to RepeatMasker that increased the speed of masking more…

A software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. MaskerAid was developed under UNIX and is written in PERL.

PILER
Desktop

PILER

An approach to de novo repeat annotation that exploits characteristic patterns…

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…

BLASTER
Desktop

BLASTER

Gathers C++ programs developed for transposable element search and their…

Gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. The suite is composed by three programs BLASTER, MATCHER and GROUPER. The…

HelitronScanner
Desktop

HelitronScanner

A two-layered local combinational variable (LCV) tool for generalized Helitron…

A two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or…

VisualRepbase
Desktop

VisualRepbase

Allows for displaying and analyzing all occurrences of transposable element…

Allows for displaying and analyzing all occurrences of transposable element families present in an annotated genome. VisualRepbase is a Java-based interface which can download selected occurrences of…

LTRharvest
Desktop

LTRharvest

An efficient software tool delivering high quality annotation of LTR…

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…

CENSOR
Web

CENSOR

A software tool which screens query sequences against a reference collection of…

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…

RepeatModeler
Desktop

RepeatModeler

Allows de novo identification and modelling. RepeatModeler is composed of two…

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…

SINEbase
Dataset

SINEbase

Allows to bring some order to the system of short interspersed elements (SINEs)…

Allows to bring some order to the system of short interspersed elements (SINEs) and to set a basis for further studies on these genomic elements. SINEBase introduces a set of formal definitions about…

maskseq
Desktop

maskseq

Writes a sequence with masked regions. maskseq can mask the sequence in a…

Writes a sequence with masked regions. maskseq can mask the sequence in a specified set of regions that characters in that region are (optionally) converted to lower case and / or (optionally)…

LTRsift
Desktop

LTRsift

A software tool for visualization and postprocessing of de novo predicted LTR…

A software tool for visualization and postprocessing of de novo predicted LTR retrotransposon annotations. LTRsift literally allows the user to ‘sift’ through a possibly large quantity of results…

LTR_par
Desktop

LTR_par

Detects full-length LTR retrotransposons in genomic sequences. LTR_par…

Detects full-length LTR retrotransposons in genomic sequences. LTR_par identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components…

HelSearch
Desktop

HelSearch

A program to identify Helitron given genomic sequences. HelSearch searches for…

A program to identify Helitron given genomic sequences. HelSearch searches for CTRRT in genomic sequence first. To narrow the results, insertion site T was included in this search. The proposed…

RepeatMasker
Desktop
Web

RepeatMasker

Screens DNA sequences for interspersed repeats and low complexity DNA…

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…

RepeatGluer
Desktop

RepeatGluer

Detects sub-repeats in a genomic sequence by using the notion of A-Bruijn…

Detects sub-repeats in a genomic sequence by using the notion of A-Bruijn graph. RepeatGluer identifies repeats and their copies into sequence to form a new sequence. These results can be observed…

REPCLASS
Desktop

REPCLASS

Automates the classification of TE (transposable elements) sequences using…

Automates the classification of TE (transposable elements) sequences using control repeat libraries. REPCLASS analysis of fungi genomes offers a comparison of TE composition at a much broader…

ELAN
Web

ELAN

An interactive tool for deducing the repeat elements in various genomes, their…

An interactive tool for deducing the repeat elements in various genomes, their site of insertion, their physio-chemical properties and their pattern of insertion. ELAN uses a combination of methods…

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