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Protocols

LTR_Finder specifications

Information


Unique identifier OMICS_07460
Name LTR_Finder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for LTR_Finder

LTR_Finder citations

 (75)
library_books

Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality

2018
Proc Natl Acad Sci U S A
PMCID: 5939082
PMID: 29678829
DOI: 10.1073/pnas.1719622115

[…] . We searched transposable elements in the tea plant genome by integrating de novo methods and homology-based methods with the prediction programs RepeatModeler (www.repeatmasker.org/RepeatModeler/), LTR_FINDER (), RepeatMasker (www.repeatmasker.org), and RepeatProteinMask (version 3.3.0; www.repeatmasker.org/RepeatProteinMask.html). Based on the repeat-masked genome, we combined three pieces of e […]

library_books

Genome Sequence of the Freshwater Yangtze Finless Porpoise

2018
Genes
PMCID: 5924555
PMID: 29659530
DOI: 10.3390/genes9040213

[…] bination of de novo prediction and homolog searches. First, for de novo predictions, we constructed a de novo repeat library with RepeatModeler (v1.0.8, http://www.repeatmasker.org/RepeatModeler) and LTR_FINDER []. Then, we used RepeatMasker v3.3.0 [] to detect additional repeats in the sequences. To search for homologs, we identified tandem repeats in our draft genome with Tandem Repeats Finder v […]

library_books

“Targeted Sequencing by Gene Synteny,” a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region

2018
Front Plant Sci
PMCID: 5882829
PMID: 29643861
DOI: 10.3389/fpls.2018.00397

[…] The BAC sequences were annotated in two steps. First, we used a method to predict long terminal repeat transposons (LTRs) via LTR_FINDER (Xu and Wang, ). Homology-based repeat analysis was performed to identify transposable elements (TEs) against Poaceae TEs available in the Repbase database (Kohany et al., ) via CENSOR. Sec […]

library_books

Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica

2018
PLoS One
PMCID: 5846777
PMID: 29529051
DOI: 10.1371/journal.pone.0193665

[…] re listed in . Because the whole genome sequence is not yet available, the repetitive sequences of C. japonica were deduced from 1,185 contigs from 159 genomic BAC clones, by using RepeatScout [] and LTR_finder [] with default settings (). The BAC clones were derived from materials unrelated to ‘Toyama-1’ []. The predicted repeat sequences were compared with other plant repeat sequences using BLAS […]

library_books

Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

2018
GigaScience
PMCID: 5893958
PMID: 29659813
DOI: 10.1093/gigascience/giy012

[…] We used RepeatProteinMask (version 4.0.6) [] in RepeatMasker (RepeatMasker, RRID:SCR_012954) to identify the repetitive sequences, before using RepeatModeller (version 1.05) [] and LTR_FINDER.x86_64-1.0.6 to construct a de novo repeat library. Additionally, repetitive elements were predicted using Tandem Repeat Finder (version 4.04). Finally, we observed that the identified repe […]

call_split

GenomeLandscaper: Landscape analysis of genome fingerprints maps assessing chromosome architecture

2018
Sci Rep
PMCID: 5773709
PMID: 29348569
DOI: 10.1038/s41598-018-19366-2
call_split See protocol

[…] transposons and satellite DNA). Hence we conduct de novo predictions of long repeats from the 1.30-Mbp segment (Supplementary Dataset ), trace homologues, and analyse evolutionary relationships.Using LTR-FINDER software, we predict 6 LTR retrotransposons (Fig. ) that are dispersed on a 98.54-Kbp cluster (from 211,266 bp to 309,809 bp) of the 1.30-Mbp segment (Supplementary Dataset ). We use each o […]

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LTR_Finder institution(s)
T-Life Research Center, Fudan University, Shanghai, China

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