LTR_Finder protocols

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LTR_Finder specifications


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

PMCID: 4718150
PMID: 26819544
DOI: 10.4137/EBO.S35158

[…] from the ncbi website (, 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 ( to search the nipponbare genome with default parameters. the output ltrs were then manually inspected to filter out incorrectly predicted […]

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 ( [] was utilized to identify full-length vl30s. sequences not corresponding to full-length vl30s were manually annotated as truncated vl30 […]

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 ( 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. […]

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 […]

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 […]

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LTR_Finder in publications

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 ( 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 (, repeatscout, and ltr-finder with default parameters. for alignment of homologous sequences to identify repeats in the assembled genome, we used repeatproteinmask and repeatmasker ( […]

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 (, ltr_finder (), repeatmasker (, and repeatproteinmask (version 3.3.0; 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, 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 […]

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

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