(Q37638210)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

review article

1 reference

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

author name string

E Lerat

series ordinal

1

1 reference

21 August 2017

language of work or name

English

0 references

publication date

25 November 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

volume

104

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

page(s)

520-533

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19935826%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/hdy.2009.165

12 February 2020

exact match

0 references

cites work

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Repseek, a tool to retrieve approximate repeats from large DNA sequences.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Basic local alignment search tool

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Detection of transposable elements by their compositional bias

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Automated de novo identification of repeat sequence families in sequenced genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

MaskerAid: a performance enhancement to RepeatMasker

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Tandem repeats finder: a program to analyze DNA sequences

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Discovering and detecting transposable elements in genome sequences

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Genetics: Junk DNA as an evolutionary force

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Characterization of three DNA transposons in the Dutch elm disease fungi and evidence of repeat-induced point (RIP) mutations.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

RAP: a new computer program for de novo identification of repeated sequences in whole genomes.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Identification of transposable elements using multiple alignments of related genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

TROLL--tandem repeat occurrence locator.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Alignment of whole genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

OMWSA: detection of DNA repeats using moving window spectral analysis

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

PILER: identification and classification of genomic repeats

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Eukaryotic transposable elements and genome evolution

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Evolutionary history of mammalian transposons determined by genome-wide defragmentation

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Identification of repeat structure in large genomes using repeat probability clouds

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Annotating large genomes with exact word matches

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Repbase Update, a database of eukaryotic repetitive elements

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

CENSOR--a program for identification and elimination of repetitive elements from DNA sequences

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Efficient algorithms and software for detection of full-length LTR retrotransposons.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Rolling-circle transposons in eukaryotes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Molecular paleontology of transposable elements in the Drosophila melanogaster genome

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Perspective: transposable elements, parasitic DNA, and genome evolution

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

mreps: Efficient and flexible detection of tandem repeats in DNA

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

TEnest: automated chronological annotation and visualization of nested plant transposable elements

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

REPuter: fast computation of maximal repeats in complete genomes.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

FORRepeats: detects repeats on entire chromosomes and between genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Codon usage and the origin of P elements

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Codon usage by transposable elements and their host genes in five species.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

A novel genome-scale repeat finder geared towards transposons.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

LTR_STRUC: a novel search and identification program for LTR retrotransposons

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Automated paleontology of repetitive DNA with REANNOTATE

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

De novo repeat classification and fragment assembly

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

An Eulerian path approach to DNA fragment assembly

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

De novo identification of repeat families in large genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Combined evidence annotation of transposable elements in genome sequences

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Bats with hATs: evidence for recent DNA transposon activity in genus Myotis

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

De novo identification of LTR retrotransposons in eukaryotic genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Empirical comparison of ab initio repeat finding programs

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The paleontology of intergene retrotransposons of maize

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Nested retrotransposons in the intergenic regions of the maize genome

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Improved repeat identification and masking in Dipterans

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Automated recognition of retroviral sequences in genomic data--RetroTector

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Genome assembly, rearrangement, and repeats

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The genome sequence of taurine cattle: a window to ruminant biology and evolution

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Evolution of genes and genomes on the Drosophila phylogeny

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Initial sequencing and analysis of the human genome

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The genome of a lepidopteran model insect, the silkworm Bombyx mori

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Initial sequencing and comparative analysis of the mouse genome

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3' tandem repeats and the poly(dA) tail

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

A clustering method for repeat analysis in DNA sequences

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

A unified classification system for eukaryotic transposable elements

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

MAK, a computational tool kit for automated MITE analysis

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE.

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

1 reference

https://api.crossref.org/works/10.1038%2FHDY.2009.165

7 January 2021