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.

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

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

RetroSeq 1.41 – Transposable Element Discovery from Next-generation sequencing data

RetroSeq 1.41

:: DESCRIPTION

RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available.

::DEVELOPER

Genomics & Genetics At The Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RetroSeq

:: MORE INFORMATION

Citation

RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong and David J. Adams
Bioinformatics (2013) 29 (3): 389-390.

Tea 0.6.2 – Transposable Element Analyzer

Tea 0.6.2

:: DESCRIPTION

Tea is a tool for detection of retrotransposition events in whole-genome sequencing data.

::DEVELOPER

Computational Genomics (PI: Peter J Park)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Tea

:: MORE INFORMATION

Citation

Eunjung Lee et al.
Landscape of Somatic Retrotransposition in Human Cancers
Science 24 August 2012: Vol. 337 no. 6097 pp. 967-971

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

Pôle Bioinformatique Lyonnais

:: 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