LTR_Finder 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 IN pipelines

 (7)
2013
PMCID: 3579696
PMID: 23356831
DOI: 10.1186/1471-2164-14-60

[…]  1e-3, matrix = blosum62, and gapped alignment. repeats were identified using fungaldb of repbase 17.04 [42], containing the repeats of pt, pgt and pst. long terminal repeats (ltr) were determined by ltr_finder [43] (e.g., red arrows in figure 3). , "mention of a trademark of a proprietary product does not constitute a guarantee of warranty of the product by the united states department of agricul […]

2013
PMCID: 3615480
PMID: 23481403
DOI: 10.1038/ncomms2596

[…] of different repeat families, as well as homologous searches to known repeat libraries (supplementary methods). ltr retrotransposons were detected by screening the genome of o. brachyantha with ltr-finder50. solo ltrs were discovered by combining analysis of homologous sequence, target site duplication and terminal motif of ltr. non-ltr retrotransposons and dna transposons were detected […]

2013
PMCID: 3616923
PMID: 23324212
DOI: 10.1186/1471-2164-14-18

[…] plant genome duplication database (http://chibba.pgml.uga.edu/duplication/). both tandemly and segmentally duplicated genes were listed in additional files 11 and 12, respectively., we executed the ltr_finder program [46] to genome-widely identify full-length sorghum ltr retrotransposons. the result was presented in additional file 13. to identify cacta dna transposon elements, we first carried […]

2013
PMCID: 3641822
PMID: 23542206
DOI: 10.1093/gbe/evt049

[…] because of the nature of the analyzed sequences (e.g., averaged from multiple loci, presence of nonfunctional but autonomous ltr elements). the pbs and ppt sequences were detected using the ltr finder software (xu and wang 2007)., specific primers were designed, usually for rt or the transposase domain of individual tes. in the first step, template dna was amplified using pcr with a mix […]

2012
PMCID: 3532108
PMID: 23285291
DOI: 10.1371/journal.pone.0053401

[…] not endangered or protected., the draft genome assembly of p. barbatus (version 3) was downloaded from the ncbi website (http://www.ncbi.nlm.nih.gov) and scanned for ltr retrotransposons with the ltr_finder program [22]. the default setting was used with the following exceptions: both the minimum ltr size and the minimum distance of ltrs (internal domain) were set at 50 bp, and the d. […]

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

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