LTR_Finder protocols

View LTR_Finder computational protocol

LTR_Finder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Transposable element prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 in pipelines

 (10)
2016
PMCID: 4718150
PMID: 26819544
DOI: 10.4137/EBO.S35158

[…] from the ncbi website (http://www.ncbi.nlm.nih.gov/)., as shown in the workflow in , as a first step to identify a novel ltr in the genome of oryza rice we used fastpcr professional 6.5 or the ltr_finder program (http://tlife.fudan.edu.cn/ltr_finder/) to search the nipponbare genome with default parameters. the output ltrs were then manually inspected to filter out incorrectly predicted […]

2016
PMCID: 4859993
PMID: 27158269
DOI: 10.1186/s13100-016-0066-8

[…] [], blat querying [] for vl30 consensus sequences from repbase [] and in-silico pcr for specific vl30s primers [] was used to annotate vl30 sequences in their respective genomic regions. the ltr-finder tool (http://tlife.fudan.edu.cn/ltr_finder/) [] was utilized to identify full-length vl30s. sequences not corresponding to full-length vl30s were manually annotated as truncated vl30 […]

2016
PMCID: 5004834
PMID: 27560652
DOI: 10.1590/1678-4685-GMB-2015-0241

[…] the genomic sequences of s. sclerotiorum class i transposable elements were obtained by searching the fungal genome database (http://www.ncbi.nlm.nih.gov/assembly/gcf_000146945.1/) and using the ltr-finder software. subsequently, the remaining copies of the elements were obtained by using the basic local alignment search tool (blast) for each previously identified element against the s. […]

2015
PMCID: 4663468
PMID: 26616172
DOI: 10.1038/srep17583

[…] of full-length retrotransposons to the gene family expansion as it is difficult to determine the contribution of non-intact retrotransposons. we identified the full-length retrotransposons by the ltr_finder program. if a gene was located within a full-length retrotransposon the gene was regarded as retrotransposon related gene. besides retrotransposons, we also surveyed the contribution […]

2014
PMCID: 4085609
PMID: 24833511
DOI: 10.3390/biology3020295

[…] from low copy regions. based on the 20-mer frequency distribution, bac clones were further categorized into low, mid and high repetitive clones., class i ltr-retrotransposons were identified using ltr-finder [] at default parameters. ltrs of each predicted retrotransposon were analyzed with j-dotter [] and clustalx [] to define their boundaries and to eliminate the false hits. the ltr-rts […]


To access a full list of citations, you will need to upgrade to our premium service.

LTR_Finder in publications

 (141)
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] a custom library. at the protein level, repeatproteinmask was used to perform an rmblast search against the te protein database. for de novo prediction, repeatmodeler (http://repeatmasker.org/) and ltr finder were used to identify de novo evolved repeats inferred from the assembled genome., we used the maker2 pipeline to predict protein-coding genes in the genome. first, the genome was repeat […]

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] version 4.0.3) and repeatproteinmask (from the repeatmasker package) programs with the default parameters []. the de novoapproach used two prediction programs, repeatmodeler [] (version 1.0.7) and ltr-finder [] (version 1.0.5), to build the de novo repeat libraries based on the genome sequences. next, contaminations and multicopy genes were removed from the libraries. then, the repeatmasker […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] to identify repeat elements in the g. elata genome. for de novo prediction of transposable elements (tes), we used repeatmodeler (http://www.repeatmasker.org/repeatmodeler.html), repeatscout, and ltr-finder with default parameters. for alignment of homologous sequences to identify repeats in the assembled genome, we used repeatproteinmask and repeatmasker (http://www.repeatmasker.org) […]

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 […]

PMCID: 5924555
PMID: 29659530
DOI: 10.3390/genes9040213

[…] 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

LTR_Finder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LTR_Finder