LTR_STRUC: a novel search and identification program for LTR retrotransposons

By E. M. McCarthy, John F. McDonald. Bioinform., 2003

360 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5155e0d8d0bdf6d7529e014a88d439d6e9c4ac03

How researchers see this paper

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In Genetics

1. Ning Jiang
2. Shujun Ou
3. Stefan Kurtz
4. Oleksiy Kohany
5. David Ellinghaus
6. Ute Willhoeft
7. Vladimir V. Kapitonov
8. Paul Klonowski

In Molecular Biology

1. Ning Jiang
2. Shujun Ou
3. Bernard Henrissat
4. Francis Martin
5. Vincent Lombard
6. A. Kohler
7. Jinfeng Chen
8. Pedro M. Coutinho

In Plant Science

1. Ning Jiang
2. Shujun Ou
3. Stephan Ossowski
4. Noah Fahlgren
5. Jinfeng Chen
6. Detlef Weigel
7. R. Balestrini
8. James C. Carrington

Citations in the corpus

• Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, methodology): “To identify full length LTR retrotransposons, a second de novo search was performed with LTR_STRUC (16).”
• 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.”
• Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, methodology): “For the identification of intact LTR-RT, many existing methods are available, such as LTR STRUC (35), LTR FINDER (10), LTRharvest (11), and LTR retriever (4).”
• LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons (2008, methodology): “LTR_STRUC has been applied to the genomes of the fruitfly Drosophila melanogaster [12], Oryza sativa (rice) [13], Mus musculus (mouse) [14] and recently Pan troglo-dytes (chimpanzee) [15].”
• Repbase Update, a database of eukaryotic repetitive elements (2005, background): “For example, LTR_struck (McCarthy and McDonald, 2003) detects new LTR retrotransposons by checking for characteristic long terminal repeats flanking the elements.”
• 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).”
• The Arabidopsis lyrata genome sequence and the basis of rapid genome size change (2011, methodology): “Intact LTR retrotransposons were identified de novo using LTR_STRU”