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

By Zhao Xu, Hao Wang. Nucleic Acids Res., 2007

2,348 citations recorded by the source corpus.

Long terminal repeat retrotransposons (LTR elements) are ubiquitous eukaryotic transposable elements. They play important roles in the evolution of genes and genomes. Ever-growing amount of genomic sequences of many organisms present a great challenge to fast identifying them. That is the first and indispensable step to study their structure, distribution, functions and other biological impacts. However, until today, tools for efficient LTR retrotransposon discovery are very limited. Thus, we developed LTR_FINDER web server. Given DNA sequences, it predicts locations and structure of full-length LTR retrotransposons accurately by considering common structural features. LTR_FINDER is a system capable of scanning large-scale sequences rapidly and the first web server for ab initio LTR retrotransposon finding. We illustrate its usage and performance on the genome of Saccharomyces cerevisiae. The web server is freely accessible at http://tlife.fudan.edu.cn/ltr_finder/.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/265e65f18cb48821850f90b53534c942e6e4d349

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Citations in the corpus

Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, methodology): “In this study, LTR-RT candidates were obtained using LTRharvest (11) with parameters ‘-minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes’ and LTR FINDER (10) with parameters ‘-D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.”
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] (2017, methodology): “The sensitivity of all existing LTR discovery tools was reported to be very high (Xu and Wang, 2007; Ellinghaus et al., 2008; You et al., 2015); however, systematic evaluation of speci ﬁ city using the whole-genome sequence length is not available.”
Genome sequence of the cultivated cotton Gossypium arboreum (2014, positive): “We used four software programs, LTR_FINDER 44 , PILER 45 , RepeatModeler and RepeatScout 46 , to generate the de novo repeat library.”
The genome of the pear (Pyrus bretschneideri Rehd.) (2013, methodology): “For structure-based search of intact TEs, LTR retrotransposons were detected by LTR_Finder (Xu and Wang 2007) and LTR_STRUC (McCarthy and McDonald 2003).”
Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality (2018, neutral): “Xu Z, Wang H (2007) LTR_FINDER: An efficient tool for the prediction of full-length LTR retrotransposons.”
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons (2008, methodology): “We also compare the quality and performance of LTRharvest to existing software tools LTR_STRUC [11], LTR_par [16], LTR_Rho [17] and LTR_FINDER [18].”
FastPCR Software for PCR Primer and Probe Design and Repeat Search (2009, methodology): “There is already some software specifically developed for identifying LTR retrotransposons – ‘LTR_STRUCT’ (McCarthy and McDonald 2003), ‘LTR_FINDER’ (Xu and Wang 2007), ‘LTR_par’ (Kalyanaraman and Aluru 2006), LTR_Rho (Rho et al.”
Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis (2018, methodology): “Complete LTR-RTs were identified for four Asteraceae species (TKS, globe artichoke, horseweed and sunflower), one Lamiaceae species (danshen) and six other model plants using the LTR-FINDER [23] (see Supplementary Fig.”
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, neutral): “Most programs were not memory intensive, with a minimum of 7.2 Mbyte (SINE-Finder), an average of 8.7 Gbyte, and a maximum of 76 Gbyte (the GRF-LTR_FINDER method) (Table S2).”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “Another frequently used tool for TE identification is LTR_FINDER [23], which is used to detect LTR retrotransposons.”