Tag: Transposable Element

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

GrainGenes

:: 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

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

Peter Park’s lab at CBMI, Harvard Medical School

:: 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

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.

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

Zlab

:: 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.

MITE-Hunter 201111 – Discovering miniature inverted-repeat Transposable Elements from Genomic Sequences

MITE-Hunter 201111

:: DESCRIPTION

 MITE-Hunter was designed to identify miniature invertedrepeat transposable elements (MITEs) as well as other small (< 2Kb, default) class 2 nonautonomous transposable elements (TEs) from genomic DNA datasets. Class 1 TEs and long TEs can’t be found by MITE-Hunter. TEs with too many mutations and mismatches in the terminal inverted repeats (TIRs) may not be detected.

::DEVELOPER

MITE-Hunter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MITE-Hunter

:: MORE INFORMATION

Citation

Nucl. Acids Res. (2010) 38 (22): e199.
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
Yujun Han and Susan R. Wessler

 

DANTE – Domain based ANnotation of Transposable Elements

DANTE

:: DESCRIPTION

DANTE uses database of Viridiplantae protein domains derived from transposable elements omains searching is accomplished engaging LASTAL alignment tool.

::DEVELOPER

Laboratory of Molecular Cytogenetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DANTE

:: MORE INFORMATION

Transposome 0.12.1 – Annotation of Transposable Element Families from Unassembled Sequence Reads

Transposome 0.12.1

:: 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

Tedna 1.3 – Transposable Element De Novo Assembler

Tedna 1.3

:: 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.

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