Institute of Bioinformatics Münster


Selected resources for Transposable Elements discovery and analyses. If you see any omission, please send a suggestion.


Link About
ACLAME A database dedicated to the collection and classification of prokaryotic mobile genetic elements (MGEs)
ConTEdb Conifer Transposable Elements Database
DPTEdb Dioecious Plants Transposable Elements Database
FishTEDB A collective database of transposable elements identified in the complete genomes of fish
GyDB An open database of viruses, mobile genetic elements (MGEs) and the genomic repeats
IS Finder The database provides a list of insertion sequences isolated from eubacteria and archae
P-MITE Plant MITE database
Repbase Repbase Update is the most commonly used database of repetitive DNA elements
RepetDB RepetDB is designed to store and retrieve detected, classified and annotated TEs
SoyTEdb The SoyTE database provides resources and information related to transposable elements (TEs) in the soybean genome
SPTEdb A database of transposable elements (TEs) in the genomes of salicaceous plants


Link About
AB-BLAST Most sensitive, fastest and flexible core BLAST engine, target your searches easier and get better results faster
BLASTER suite Developed for transposable element search and their annotation in large eukaryotic genome sequence
Censor Compares and masks protein or nucleotide sequences
HERVd Simple and fast environment for screening human genome for HERVs (=Human endogenous retroviruses)
IS Finder Provides a list of insertion sequences isolated from eubacteria and archae
LTR_FINDER An efficient program for finding full-length LTR retrotranspsons in genome sequences
LTRdigest Automated annotation of internal features of LTR retrotransposons
LTRharvest De novo detection of LTR retrotransposons
LTR_STRUC Scans nucleotide sequence files for LTR retrotransposons
MGEScan-LTR Long terminal repeat (LTR) retroelements discovery
MGEScan-nonLTR Non-long terminal repeat (non-LTR) retrotransposons discovery
microTranspoGene The influence of Transposed Elements (TEs) on the biogenesis of microRNAs
MITE-Hunter Discovering miniature inverted-repeat transposable elements from genomic sequences
PClouds The P-clouds package is designed to identify repeat structure in large eukaryotic genomes using oligonucleotide counts.
PILER A software for analyzing repetitive DNA found in genome sequences
REannotate Automated Molecular Paleontology of Complex DNA Repeats
RECON A package for automated de novo identification of repeat families from genomic sequences
RepSeek A two-steps method (seed detection followed by their extensions) that detects approximate repeats
RepeatFinder Fnding repetitive sequences complete and draft genomes
RepeatMasker Screens DNA sequences for interspersed repeats and low complexity DNA sequences
RepeatModeler A de-novo repeat family identification and modeling package
RepeatRunner A CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements
repeat-match Ultra-fast alignment of large-scale DNA and protein sequences
REPET The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale
RepMiner Takes a graph theory approach to the classification and assembly of the repetitive fraction of genomic sequence data
REPuter Provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes
RetroMap An application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner
SMaRTFinder A command line tool to search biosequences for structured motifs
Spectral Repeat Finder Find repeats through an analysis of the power spectrum of a given DNA sequence
Tallymer A collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
TARGeT Tree Analysis of Related Genes and Transposons
TEclass Classifies unknown transposable element (TE) consensus sequences using machine learning approach
TE Displayer TE Displayer can be used to retrieve genetic polymorphisms caused by transposable elements (TEs) in large-genomic datasets and present the results on virtual gel images
TESD Provides a complete application that allows modellers to implement other models of TE dynamics
TESeeker TESeeker implements an automated homology-based approach for identifying transposable elements
TinT Considering the high frequency of transposed elements they contribute significantly to genome evolution and encrypt valuable information about the phylogenetic relationships of their host species.
TIPseqHunter Identifies insertion sites with high precision and reliability
T-lex A computational pipeline to detect presence and/or absence of annotated individual transposable elements (TEs) in sequenced genomes using NGS data
TRANSPO Searching for Transposons with known TIR
TranspoGene The influence of Transposed Elements (TEs) on the transcriptome of seven metazoan species
Transposon-PSI An analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements
TRAP Tandem Repeats Analysis Program
TRF Tandem repeats finder: a program to analyze DNA sequences
TROLL Tandem Repeat Occurrence Locator
TSDfinder A PERL script to detect target site duplications
Vmatch A versatile software tool for efficiently solving large scale sequence matching tasks.
2019-03-07 16:56