TESD 1.0 – Transposable Element Simulator Dynamics

TESD 1.0

:: DESCRIPTION

TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.

::DEVELOPER

TESD team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  TESD

:: MORE INFORMATION

Citation:

Grégory Deceliere, Yann Letrillard, Sandrine Charles and Christian Biémont
TESD: a transposable element dynamics simulation environment
Bioinformatics November 1, 2006 22:2702-2703

TeXP v1.0 – Quantifying Abundances of Transposable Elements transcripts from RNA-Seq data

TeXP v1.0

:: DESCRIPTION

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TeXP

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2019 Aug 19;15(8):e1007293. doi: 10.1371/journal.pcbi.1007293. eCollection 2019 Aug.
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

T-lex 2.2.2 – Assessment of Transposable Element Presence in Next-generation Sequencing data

T-lex 2.2.2

:: DESCRIPTION

The T-lex pipeline identifies reads that indicate the presence or absence of individual TEs with high specificity. Handling a large amount of data, it can return the frequency of a TE in the population.

::DEVELOPER

The Petrov Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 T-lex

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Fiston-Lavier AS, Barrón MG, Petrov DA, González J

Fiston-Lavier AS, Carrigan M, Petrov DA and Gonzalez J.
T-LEX: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Nuc. Acids. Res. 2011 Mar 1;39(6):e36. Epub 2010 Dec 21

Transposome 0.09.7 – Annotation of Transposable Element Families from Unassembled Sequence Reads

Transposome 0.09.7

:: DESCRIPTION

Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data.

::DEVELOPER

Evan Staton

:: SCREENSHOTS

N/A.

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Transposome

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Feb 1. pii: btv059. [Epub ahead of print]
Transposome: A toolkit for annotation of transposable element families from unassembled sequence reads.
Staton SE1, Burke JM

TEMP v1.04 – Analyzing Transposable Element Polymorphism in Populations

TEMP v1.04

:: DESCRIPTION

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

::DEVELOPER

Jiali Zhuang (jiali.zhuang@umassmed.edu) and Jie Wang (jie.wangj@umassmed.edu) @ ZLab, University of Massachusetts Medical School, Worcester, MA, USA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TEMP

:: MORE INFORMATION

Citation

TEMP: a computational method for analyzing transposable element polymorphism in populations.
Zhuang J, Wang J, Theurkauf W, Weng Z.
Nucleic Acids Res. 2014 Jun;42(11):6826-38. doi: 10.1093/nar/gku323.

TASR 1.1 – Annotate Transposable Elements using siRNAs Mapping

TASR 1.1

:: DESCRIPTION

TASR (Transposon Annotation using Small RNAs) is a bioinformatic pipeline that can annotate Transposable elements using siRNAs mapping

::DEVELOPER

TASR team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TASR

:: MORE INFORMATION

Citation

A new approach for annotation of transposable elements using small RNA mapping.
El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA.
Nucleic Acids Res. 2015 Jul 27;43(13):e84. doi: 10.1093/nar/gkv257.

VisualTE 1.02 – Graphical Interface for Transposable Element Analysis at Genomic Scale

VisualTE 1.02

:: DESCRIPTION

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

::DEVELOPER

Biophotonics Lab

:: SCREENSHOTS

VisualTE

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java Runtime Environment (JRE)

:: DOWNLOAD

 VisualTE

:: MORE INFORMATION

Citation

VisualTE: a graphical interface for transposable element analysis at the genomic scale.
Tempel S, Talla E.
BMC Genomics. 2015 Feb 27;16:139. doi: 10.1186/s12864-015-1351-5.

Tedna 1.2.2 – Transposable Element De Novo Assembler

Tedna 1.2.2

:: DESCRIPTION

Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.

::DEVELOPER

INRA, URGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Tedna

:: MORE INFORMATION

Citation

Tedna: a Transposable Element De Novo Assembler.
Zytnicki M, Akhunov E, Quesneville H.
Bioinformatics. 2014 Jun 3. pii: btu365.

RJPrimers 1.0 – Transposable Element Junction based PCR Primer Design

RJPrimers 1.0

:: DESCRIPTION

RJPrimers is a high-throughput software tool to identify unique repeat junction and design TE-based primers for high-throughput marker development. This tool first identifies potentially unique repeat junctions using BLAST against fully annotated repeat databases and a repeat junction finding algorithm, and then designs TE based primers using Primer3 and BatchPrimer3.

::DEVELOPER

Plant Genome Research Program: Physical Mapping of the Wheat D genome

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak and Yong Q. Gu.
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
Nucl. Acids Res. (2010) 38 (suppl 2): W313-W320. doi:10.1093/nar/gkq425