1 - 50 of 65 results

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.

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.

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.

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.

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.

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.

Genome ARTIST / Genome ARtificial Transposon Insertion Site Tracker

forum (1)
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.

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.

Red

star_border star_border star_border star_border star_border
star star star star star
(2)
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.

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.

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.

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.

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.

RJPrimers

Obsolete
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.

LTR Annotator

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 annotations such as internal domains, primer binding site (PBS), poly purine tract (PPT) sequences, copy numbers of identified intact elements and solo-LTRs, divergence estimates based on LTR pairs and presence of genes in the neighborhoods of identified LTR elements. It also allows to perform comparative analyses of LTRs across multiple sequenced plant genomes using common parameters.

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).

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.

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.

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.