Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi

(2009) Yong Chen et al.   GENE

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

(2009) Yujun Han et al.   NUCLEIC ACIDS RESEARCH

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

(2009) James C Estill et al.   Plant Methods

Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE

(2009) G. Yang et al.   SCIENCE

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Identification of repeat structure in large genomes using repeat probability clouds

(2008) Wanjun Gu et al.   ANALYTICAL BIOCHEMISTRY

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)

(2008) Thomas D Otto et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Automated paleontology of repetitive DNA with REANNOTATE

(2008) Vini Pereira   BMC GENOMICS

Computational prediction and molecular confirmation of Helitron transposons in the maize genome

(2008) Chunguang Du et al.   BMC GENOMICS

Empirical comparison of ab initio repeat finding programs

(2008) S. Saha et al.   NUCLEIC ACIDS RESEARCH

Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

(2008) Surya Saha et al.   Tropical Plant Biology

The canine hookworm genome: Analysis and classification of Ancylostoma caninum survey sequences

(2007) Sahar Abubucker et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY