Tag: Repeats

REPET 3.0 / PASTEClassifier 2.0 – Detection, Annotation and Analysis of Repeats in Genomic Sequences

REPET 3.0 / PASTEClassifier 2.0

:: DESCRIPTION

REPET is a software of detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements

PASTEClassifier  classifies TEs by searching for structural features and similarities.

::DEVELOPER

URGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 REPET , PASTEC

:: MORE INFORMATION

Citation

PASTEC: An Automatic Transposable Element Classification Tool.
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H.
PLoS One. 2014 May 2;9(5):e91929. doi: 10.1371/journal.pone.0091929.

Flutre T, Duprat E, Feuillet C, Quesneville H.
Considering transposable element diversification in de novo annotation approaches.
PLoS One. 2011 Jan 31;6(1):e16526.

airpg 1.1.4 – Automatically Accessing the inverted Repeats of Archived Plastid Genomes

airpg 1.1.4

:: DESCRIPTION

airpg is an Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Python

:: DOWNLOAD

airpg

:: MORE INFORMATION

Citation

Mehl T, Gruenstaeudl M.
airpg: automatically accessing the inverted repeats of archived plastid genomes.
BMC Bioinformatics. 2021 Aug 21;22(1):413. doi: 10.1186/s12859-021-04309-y. PMID: 34418956; PMCID: PMC8379869.

findIR – Detection of Perfect Overlapping and Nested Inverted Repeats in DNA Sequences

findIR

:: DESCRIPTION

Palindrome (also known as findIR) is a MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • MatLab

:: DOWNLOAD

 Palindrome

:: MORE INFORMATION

Citation

A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences.
Sreeskandarajan S, Flowers MM, Karro JE, Liang C.
Bioinformatics. 2013 Nov 30.

TRDistiller – Tandem Repeats Detection

TRDistiller

:: DESCRIPTION

TRDistiller is a rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs.

::DEVELOPER

BiSMM – Structural Bioinformatics and Molecular Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

 TRDistiller

:: MORE INFORMATION

Citation

J Struct Biol. 2014 Jun;186(3):386-91. doi: 10.1016/j.jsb.2014.03.013. Epub 2014 Mar 26.
TRDistiller: a rapid filter for enrichment of sequence datasets with proteins containing tandem repeats.
Richard FD, Kajava AV

SRF 1.1 – Find Repeats through an analysis of the power Spectrum of a given DNA Sequence

SRF 1.1

:: DESCRIPTION

 SRF (Spectral Repeat Finder) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not

::DEVELOPER

SRF Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jun 12;20(9):1405-12. Epub 2004 Feb 19.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
Sharma D, Issac B, Raghava GP, Ramaswamy R.

REPdenovo V2 – A tool to Construct Repeats directly from Raw Reads

REPdenovo V2

:: DESCRIPTION

REPdenovo is a new method which assembles repeat sequences directly from raw shotgun sequencing data.

::DEVELOPER

Yufeng Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 REPdenovo

:: MORE INFORMATION

Citation:

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.
Chu C, Nielsen R, Wu Y.
PLoS One. 2016 Mar 15;11(3):e0150719. doi: 10.1371/journal.pone.0150719.