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MGEScan
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 suited for data visualization in general data formats. MGEScan is a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speedup of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud.
phRAIDER / pattern-hunter based Rapid Ab Initio Detection of Elementary Repeats
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 PatternHunter spaced seed model, allowing for greater sensitivity in the presence of genomic substitutions. As compared with the premier tool in the literature, RepeatScout, phRAIDER shows an average 10× speedup on any single human chromosome and has the ability to process the whole human genome in just over three hours.
Red
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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 RepeatScout and ReCon are sensitive to transposons, and WindowMasker to simple repeats. Red performed consistently well on seven genomes; the other tools performed well only on some genomes. Red is much faster than RepeatScout and ReCon and has a much lower false positive rate than WindowMasker.
RJPrimers
Identifies repeat junctions and then designs repeat junction marker (RJM) primers. RJPrimers is a high-throughput computational tool that employs a BLASTN search and a repeat junction finding algorithm. It includes three contiguous operational steps, a BLASTN search against a repeat database, repeat junction identification and primer design. Its performance depends on the number of sequences and their sizes, the number of repeat junctions in the sequences, the size of the repeat database selected, and the speed of the computer.
RTAnalyzer
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 designed to search for small non-coding RNAs that possess the signature of a sequence that was inserted in the genome by L1. It can help to understand the L1 mechanism in non-autonomous retro-transposition and to explain the sharp differences observed between the pseudogene frequencies of different small non-coding RNAs, as well as differences between species.
LTR_STRUC / LTR retrotransposon structure program
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 retrotransposon families having low sequence homology to known queries or families with atypical structure (e.g. non-autonomous elements lacking canonical retroviral ORFs) and is thus a discovery tool that complements established methods. LTR_STRUC finds LTR retrotransposons using an algorithm that encompasses a number of tasks that would otherwise have to be initiated individually by the user. For each LTR retrotransposon found, LTR_STRUC automatically generates an analysis of a variety of structural features of biological interest.
iMapper / Insertional Mutagenesis Mapper
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 derived from the insertional mutagen. The software then identifies and removes contaminating sequences derived from chimeric genomic fragments, vector or the transposon concatamer and then presents the clipped sequence reads to a sequence mapping server which aligns them to an Ensembl genome. Insertion sites can then be navigated in Ensembl in the context of genomic features such as gene structures. iMapper also generates test-based format for nucleic acid or protein sequences (FASTA) and generic file format (GFF) files of the clipped sequence reads and provides a graphical overview of the mapped insertion sites against a karyotype. iMapper is designed for high-throughput applications and can efficiently process thousands of DNA sequence reads.
Greedier
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 identifies the local similarities between the repeat library and the target genome. Greedier then builds graphs from this comparison output. In each graph, a vertex denotes a similar subsequence pair. Edges denote pairs of subsequences that can be connected to form higher similarities. In the second pass, Greedier traverses these graphs greedily to find matches to individual repeat units in the repeat library. It computes a fitness value for each such match denoting the similarity of that match. Matches with fitness values greater than a cutoff are removed, and the rest of the genome is stitched together. The similarity cutoff is then gradually reduced, and the iteration is repeated until no hits are returned from the comparison.
InFiRe / Insertion Finder via Restriction digest
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 bacterial DNA yields unique pattern of DNA fragments with defined sizes. Transposon insertion changes the size of the hosting DNA fragment by a known number of base pairs. The exact sizes of this fragment can be determinate by Southern blot hybridization and identified with subsequent computational analysis.
retrotransposons-spread
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 degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Various functions have been implemented to simulate this spread as well as graphic representations. Finally, a first method for estimating the parameters of this propagation model has been proposed and applied to the spread of transposable elements corresponding to the ROO, GYPSY, and DM412 elements in a chromosome of Drosophila melanogaster.
LTRsift
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 LTRharvest and/or LTRdigest, which it was designed to work with. However, it relies on standard data formats and can also work on results from other tools, given that the input data are appropriately formatted. LTR retrotransposons can be assigned both automatically and manually to groups considered putative families, which can then serve as a basis for comprehensive sequence library preparation. Relying on a common GUI toolkit from the open source world, the user interface is familiar to everyday computer users. LTRsift is efficient enough to allow work with large datasets consisting of up to tens of thousands of candidates on standard desktop hardware, making it likely to be used by life scientists preferring a visual, exploratory hands-on approach to dealing with result data.
LTRtype
Mines increasingly sequenced genomes by using multithreading technologies. LTRtype is a software program to identify different types of structurally complex long terminal repeat (LTR) retrotransposons and characterize their nested insertions in the genome. This package can be used as an automated methodology for efficiently genome-wide mining structurally different types of LTR retrotransposon elements that may have largely contributed to the function and evolution of LTR retrotransposons in the eukaryote genomes.
detectMITE
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 genomes. detectMITE adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, detectMITE detects MITEs on a genome-wide scale more accurately, comprehensively, and efficiently than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known and novel MITEs with a complete structure and full-length copies in the genome.
Genome ARTIST / Genome ARtificial Transposon Insertion Site Tracker
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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 for the classical alignment algorithms and may be exploited for checking the specificity of short sequences as primers or probes. Last but not the least, aficionados of different model organisms may use the abilities of Genome ARTIST by loading other genomes and/or specific transposons.
REPCLASS
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 evolutionary scale and can classify accurately virtually any known TE types. The input file for the program is a single text file containing the DNA sequences to be classified. REPCLASS development’ will make it possible to rapidly characterize TE landscapes in a large and diverse sample of eukaryotic species.
VisualTE
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 repeat data. Result analyses are displayed in several graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes’ features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms.
DAWGPAWS
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 annotation of genomic sequence contigs. These programs generate the multiple tracks of annotation evidence that can be computationally combined or manually curated to generate gene models and richly annotated transposable element predictions. The computation of the annotation evidence tracks can be distributed across nodes in a high-performance computing environment providing a scalability that makes this a pipeline to annotate whole-genome sequences (PAWS). The flexibility of evidences that can be generated by DAWGPAWS allows it to be applied to any eukaryotic genome annotation effort.
PASTEC
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 orders of autonomous TEs defined in Wicker’s classification plus three orders of non-autonomous TEs (LARD, TRIM and MITE). The software is also designed to filter out false-positive repeated sequences identified by de novo approaches and to classify and recognize incomplete and potentially chimeric TEs.
EnHERV / Human Endogenous Retrovirus Enrichment Tool
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 enrichment analysis between selected Human endogenous retrovirus (HERV) characteristics. It can identify certain HERV characteristic that statistically significant of enrichment in specified gene list especially for gene expression data. It offers a database designed for not only searching HERV neighboring gene.
GREAM / Genomic Repeat Element Analyzer for Mammals
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 other neighborhoods across a set of query genes from a species, b) specific chromosomal regions of a species, and c) the promoters or other neighborhoods of orthologous genes from different species. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. GREAM allows to analyze the distribution of repeat elements in the gene neighborhood region of seventeen mammalian species (such as Human, Mouse, Rat, Dog, Monkey, Gorilla, Gibbon, Cow, Marmoset, Opposum, Platypus, Elephant, Orangutan, Rabbit, Horse, Pig and Chimpanzee).
LTRharvest
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.
VisualRepbase
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 given families on the chromosome, and present the localization of these occurrences with regard to gene annotations and other families of transposable elements in Repbase. In addition, it has several features for saving the graphical representation of occurrences, saving all sequences in FASTA format, and searching and saving all annotated genes that are surrounded by these occurrences.
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 distinguish this algorithm from that of current software--(i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in run-time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility.
LTRclassifier
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 various TE databases, and shown to be robust and fast. It can annotate quickly (less than 2h for 4,000 LTR retrotransposon sequences), and with a high confidence (95 to 97,5% of specificity), the frames for any LTR retrotransposon sequence, complete element or not. The tool will provide informations about 2 types of abnormal structures to improve annotation: (i) detection of opposite strands as coding, (ii) detection of motifs from copia and gypsy.
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Transpogene
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 information regarding specific type and family of the Transposed elements, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern.
SINEbase
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 SINEs. More than 170 families have been counted (concerning animals, flowering, plants, and green algae) on the base. These families are classified according to the modular structure of their nucleotide sequences. The website can be used in two ways: (1) exploring the database, (2) analyzing candidate SINE sequences.
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