Repetitive DNA analytical step
A CLAssification of Mobile genetic Elements
A CLAssification of Mobile genetic Elements
ACLAME
A database dedicated to the collection and classification of mobile genetic elements…
A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic…
BLASTER
BLASTER
Gathers C++ programs developed for transposable element search and their annotation in…
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 results of BLASTER can be treated further by the…
Bombyx mori Transposable Elements Database
Bombyx mori Transposable Elements Database
BmTEdb
A collective database of transposable elements (TEs) in the silkworm (Bombyx mori)…
A collective database of transposable elements (TEs) in the silkworm (Bombyx mori) genome. Users are entitled to browse, search and download the sequences in the database. Sequence analyses such as BLAST, HMMER and EMBOSS GetORF were also provided…
Buffalo MicroSatellite Database
Buffalo MicroSatellite Database
BuffSatDB
A web based relational database of microsatellite markers, developed using PHP and MySQL…
A web based relational database of microsatellite markers, developed using PHP and MySQL database.
Catalogue of Genes Affected by Transposable…
Catalogue of Genes Affected by Transposable Elements
C-GATE
A catalogue of transposable element (TE) exaptation events, including information on the…
A catalogue of transposable element (TE) exaptation events, including information on the TE copy but also on the affected gene. C-GATE is interactive and allows users to include missed or new TE exaptation data. C-GATE provides a graphic…
CENSOR
CENSOR
A software tool which screens query sequences against a reference collection of repeats…
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.
ChloroMitoSSRDB
ChloroMitoSSRDB
A comprehensive online database of all SSRs (Simple Sequence Repeats) or STRs (Short…
A comprehensive online database of all SSRs (Simple Sequence Repeats) or STRs (Short Tandem Repeats) or Microsatellites from all sequenced Chloroplast and Mitochondrial genomes available so far across all the clades of life. SSRs are considered as…
ChloroSSRdb
ChloroSSRdb
Provides information of all the three types (perfect, imperfect and compound) of simple…
Provides information of all the three types (perfect, imperfect and compound) of simple sequence repeats (SSRs). In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers,…
CicArMiSatDB
CicArMiSatDB
A web resource for exploring microsatellite (Simple Sequence Repeat) markers information…
A web resource for exploring microsatellite (Simple Sequence Repeat) markers information for Chickpea.
Database of Retrotransposon Insertion…
Database of Retrotransposon Insertion Polymorphisms
dbRIP
An integrated and interactive database of human retrotransposon insertion polymorphisms…
An integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). Users can query the database by a variety of means and have access to the detailed information related to a RIP, including detailed insertion sequences…
DAWGPAWS
DAWGPAWS
A tool for discovering the location of the genes and transposable elements in eukaryotic…
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 distributed annotation working group (DAWG) in the…
Dfam
Dfam
An open access database of families of repetitive DNA elements, in which each family is…
An open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). Dfam families include retrotransposons, DNA transposons, interspersed…
DomainOrganizer
DomainOrganizer
Proposes a synthetic view of a set of DNA sequences by providing both a segmentation of…
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, finds the domains in the alignment and searches the…
ELAN
ELAN
An interactive tool for deducing the repeat elements in various genomes, their site of…
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 ranging from sequence comparison to pattern…
Eukaryotic MicroSatellite database
Eukaryotic MicroSatellite database
EuMicroSatdb
A web based relational database for easy and efficient positional mining of…
A web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes.
euL1db
euL1db
Provides a curated and comprehensive summary of L1-HS insertion polymorphisms identified…
Provides a curated and comprehensive summary of L1-HS insertion polymorphisms identified in healthy or pathological human samples and published in peer-reviewed journals. euL1db will help understanding the link between L1 retrotransposon insertion…
FAIR
FAIR
A computing engine to find all internal repeats.
A computing engine to find all internal repeats.
FishMicrosat
FishMicrosat
A microsatellite database of commercially important fishes and shellfishes of the Indian…
A microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.
FREP
FREP
Contains 31,396 RepeatMasker-identified non-redundant variant repeat sequences derived…
Contains 31,396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation,…
Genome ARtificial Transposon Insertion Site…
Genome ARtificial Transposon Insertion Site Tracker
Genome ARTIST
A bioinformatics tool originally developed in order to allow a rapid detection of…
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 derivatives. To some extent, Genome ARTIST is an alternative…
Greedier
Greedier
An iterative algorithm to find repeats in a target genome given a repeat library.…
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 iteration consists of two passes. In the first pass, it…
Gypsy Database
Gypsy Database
GyDB
A research project devoted to the evolutionary dynamics of viruses and transposable…
A research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). GyDB is a long-term project that is continuously progressing, and that owing to…
HelitronScanner
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 structure. HelitronScanner identified 64,654 Helitrons…
HelSearch
HelSearch
A program to identify Helitron given genomic sequences. HelSearch searches for CTRRT in…
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 Helitron end (helend) structure is composed of a…
HomologMiner
HomologMiner
Identifies homologous groups applicable to genome sequences that have been properly…
Identifies homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats. HomologMiner incorporates several new methods: a new abstract definition of consistent…
Horizontal Transferred of Transposable elements…
Horizontal Transferred of Transposable elements Database
HTT-DB
Allows easy access to all known cases of horizontal transfer of transposable elements…
Allows easy access to all known cases of horizontal transfer of transposable elements (HTT) reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using TEs and/or host…
Human Endogenous RetroVirus database
Human Endogenous RetroVirus database
HERVd
Provides complex information on and analysis of retroviral elements found in the human…
Provides complex information on and analysis of retroviral elements found in the human genome. HERVd can be used for searches of individual HERV families, identification of HERV parts, graphical output of HERV structures, comparison of HERVs and…
Insertion Finder via Restriction digest
Insertion Finder via Restriction digest
InFiRe
Allows for the computational identification of transposon insertion sites in known…
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 that restriction endonucleases digestions of…
Insertion Sequence semi-automatic genome…
Insertion Sequence semi-automatic genome annotation
ISsaga
Provides computational tools and methods for high-quality insertion sequence (IS)…
Provides computational tools and methods for high-quality insertion sequence (IS) annotation. ISsaga uses established ISfinder annotation standards and permits rapid processing of single or multiple prokaryote genomes. ISsaga provides general…
Insertional Mutagenesis Mapper
Insertional Mutagenesis Mapper
iMapper
A web application for the efficient analysis of insertion site sequence reads against…
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 sequence to remove the linker and sequences…
INTEGRALL
INTEGRALL
A freely available tool developed in order to provide an easy access to integron’s DNA…
A freely available tool developed in order to provide an easy access to integron’s DNA sequences and genetic arrangements. INTEGRALL contains more than 7000 integron sequences and provides a public genetic repository for sequence data and…
Inverted Repeats Finder
Inverted Repeats Finder
IRF
A prototype tool for identifying approximate inverted repeats in nucleotide sequences…
A prototype tool for identifying approximate inverted repeats in nucleotide sequences that is similar in concept to the Tandem Repeats Finder. Candidate IRs are detected by finding short, exact, reverse-complement matches of 4-7 nt (k-tuples)…
Leishmania Microsatellite Database
Leishmania Microsatellite Database
LeishMicrosatDB
To collect, organize and analyze genomic sequence repeats from various Leishmania species.
To collect, organize and analyze genomic sequence repeats from various Leishmania species.
LTR retrotransposon structure program
LTR retrotransposon structure program
LTR_STRUC
Identifies and automatically analyzes LTR retrotransposons in genome databases by…
Identifies and automatically analyzes LTR retrotransposons in genome databases by searching for structural features characteristic of such elements. LTR_STRUC has significant advantages over conventional search methods in the case of LTR…
LTR_Finder
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 large-scale sequences rapidly and the first web server for…
LTR_par
LTR_par
Detects full-length LTR retrotransposons in genomic sequences. LTR_par identifies regions…
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 distinguish this algorithm from that of current…
LTRdigest
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 retrotransposon-associated protein domains as well as primer binding…
LTRharvest
LTRharvest
An efficient software tool delivering high quality annotation of LTR retrotransposons.…
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…
LTRsift
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 from a prediction and annotation software like…
Maize Repeat Database version 4.0
Maize Repeat Database version 4.0
Maize Repeat Database
Contains maize repeat sequences. Maize Repeat Database exists as three separate files:…
Contains maize repeat sequences. Maize Repeat Database exists as three separate files: “characterized repeats” (623 sequences), uncharacterized repeats” (21,133 sequences), and “RECON-predicted repeats” (5035 sequences).
Maize transposable element database
Maize transposable element database
Maize TE database
Stores information about transposable elements (TEs). In addition to identifying all TEs…
Stores information about transposable elements (TEs). In addition to identifying all TEs in maize, this project will pay particular attention to the characterization of TEs such as Pack-MULEs and Helitrons that routinely capture and amplify gene…
Mapping and Analysis of Sirevirus Elements
Mapping and Analysis of Sirevirus Elements
MASiVE
An expertly built tool for the large-scale, yet sensitive and highly accurate, discovery,…
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 sequences. Validation was based on the recently…
Mapping and Analysis of SireVirus Elements…
Mapping and Analysis of SireVirus Elements database
MASiVEdb
A collective and systematic resource of Sireviruses in plants. MASiVEdb is unlike any…
A collective and systematic resource of Sireviruses in plants. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of…
MaskerAid
MaskerAid
A software enhancement to RepeatMasker that increased the speed of masking more than…
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.
MGEScan
MGEScan
MGEScan-LTR and MGEScan-nonLTR are successfully used programs for identifying long…
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 supported by easy-to-use interfaces nor well…
Microsatellite Analysis Server
Microsatellite Analysis Server
MICAS
An interactive user-friendly web-based analysis server to find non-redundant…
An interactive user-friendly web-based analysis server to find non-redundant microsatellites of a selected bacterial or archeal genome sequence.
MITE Digger
MITE Digger
Genome wide retrieval of MITEs.
Genome wide retrieval of MITEs.
MITE-Hunter
MITE-Hunter
A program pipeline that can identify MITEs as well as other small Class 2 non-autonomous…
A program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets.
MitoSatPlant
MitoSatPlant
A repository of plant mitochondrial SSRs (mtSSRs). It contains information for perfect,…
A repository of plant mitochondrial SSRs (mtSSRs). It contains information for perfect, imperfect and compound SSRs mined from 92 mitochondrial genomes of green plants, available at NCBI (as of 1 Feb 2014).
MnTEdb
MnTEdb
To better understand the roles of TEs in structural, functional and evolutionary dynamics…
To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database was constructed. MnTEdb was built based on a detailed and accurate…
Olive Genetic Diversity Database
Olive Genetic Diversity Database
OGDD
It is a genetic, morphologic and chemical database of worldwide olive tree and oil having…
It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their…
P-clouds
P-clouds
Identifies repeat structures in large eukaryotic genomes using oligonucleotide counts.…
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 66%-69% of the human genome is repetitive or…
Pigeonpea Microsatellite database
Pigeonpea Microsatellite database
PIPEMicroDB
A web based relational database of microsatellites present in the whole genome sequence.
A web based relational database of microsatellites present in the whole genome sequence.
PILER
PILER
An approach to de novo repeat annotation that exploits characteristic patterns of local…
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…
Plant MITE databases
Plant MITE databases
P-MITE
A series of databases was constructed to host all MITE sequences from the 41 plant…
A series of databases was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used…
Plant Repeat Databases
Plant Repeat Databases
Assist in the compilation and identification of repeat sequences in plant genomes.
Assist in the compilation and identification of repeat sequences in plant genomes.
PLOTREP
PLOTREP
It is designed to be used by anyone who would like to identify interspersed repetitive…
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 repeat and allows rapid visual inspection of the…
Polymorphic Simple Sequence Repeats database
Polymorphic Simple Sequence Repeats database
PSSRdb
Relational Database which provides the information of the Polymorphic Simple Sequence…
Relational Database which provides the information of the Polymorphic Simple Sequence Repeats in prokaryotes.
Prokaryotic Repeats Annotation Program
Prokaryotic Repeats Annotation Program
PRAP
Automates the analysis of repeats in both finished and draft genomes. It is aimed at…
Automates the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared with the major existing repeat finding tools, PRAP exhibits competitive or better…
PTGBase
PTGBase
A public database to collect plant genes generated by tandem duplication mechanism in the…
A public database to collect plant genes generated by tandem duplication mechanism in the process of plant evolution. PTGBase delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly…
Red
Red
A repeat-detection tool capable of labeling its training data and training itself…
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 repeats; in contrast, available tools such as…
Repbase
Repbase
A reference database of eukaryotic repetitive DNA, which includes prototypic sequences of…
A reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made…
RepeatMasker
RepeatMasker
Screens DNA sequences for interspersed repeats and low complexity DNA sequences. The…
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…
RepeatScout
RepeatScout
A tool to discover repetitive substrings in DNA.
A tool to discover repetitive substrings in DNA.
Repseek
Repseek
An implementation of a two-steps method (seed detection followed by their extension) that…
An implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats.
REPuter
REPuter
Detection of various types of repeats is provided together with an evaluation of…
Detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.
Short Tandem Repeat DNA Internet DataBase
Short Tandem Repeat DNA Internet DataBase
STRBase
An information resource for the forensic DNA typing community with details on commonly…
An information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA…
SugarBeet Microsatellite Marker Database
SugarBeet Microsatellite Marker Database
SBMDb
Using a computationally intensive in silico approaches, we mined and catalog the 145 K…
Using a computationally intensive in silico approaches, we mined and catalog the 145 K short tandem repeats (STR) markers and built the first whole genome based STR database. With the marker information present in the SBMDb, the linkage map’s…
Tandem Repeat Annotation Library
Tandem Repeat Annotation Library
TRAL
Makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes…
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…
Tandem Repeats DataBase
Tandem Repeats DataBase
TRDB
A public repository of information on tandem repeats in genomic DNA.
A public repository of information on tandem repeats in genomic DNA.
Tandem Repeats Finder
Tandem Repeats Finder
TRF
An algorithm for finding tandem repeats in DNA sequences without the need to specify…
An algorithm for finding tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. TRF uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori…
TAndem Splice Site DataBase
TAndem Splice Site DataBase
TassDB
Stores extensive data about alternative splice events at donors and acceptors, both…
Stores extensive data about alternative splice events at donors and acceptors, both confirmed and unconfirmed cases. TassDB offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific…
The Microorganisms Tandem Repeats Database
The Microorganisms Tandem Repeats Database
An internet-based resource to help develop and perform tandem repeats based bacterial…
An internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison…
Transposon Annotation using Small RNAs
Transposon Annotation using Small RNAs
TASR
De novo annotation of transposable elements (TEs) in Arabidopsis, rice and soybean. The…
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 evolutionary role of TEs in molding and regulating…
TRedD
TRedD
Contains the tandem repeats found in the human genome. The database is publicly available…
Contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition…
VisualRepbase
VisualRepbase
Allows for displaying and analyzing all occurrences of transposable element families…
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 transposable elements, show the distribution of…
VisualTE
VisualTE
A JAVA stand-alone graphical interface that allows users to visualize and analyze all…
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 elements and genomic information from annotation and…
VNTRDB
VNTRDB
A freely accessible variable number tandem repeat database (VNTRDB) that is intended to…
A freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can…