PILER: identification and classification of genomic repeats

By Robert C. Edgar, Eugene W. Myers. Intelligent Systems in Molecular Biology, 2005

619 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/9368b2b1d1eef4675a0670611e10143c3595ba6a

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Citations in the corpus

Empirical comparison of ab initio repeat finding programs (2008, methodology): “Recon and PILER use sequence self-comparison approaches in which initial alignment is conducted using the tools WU-BLAST (http://blast.wustl.edu/) and PALS ( 20 ), respectively.”
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats (2007, methodology): “It is based on the Piler [20] program, which utilizes alignment matrices for detecting contiguous repeats.”
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. (2007, methodology): “This file can be directly imported into genome browsers and databases that adhere to Sequence Ontology (Eilbeck et al. 2005) and GMOD (http://www.gmod.org) standards.”
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma (2011, methodology): “We scanned the Trichoderma genomes with the de novo repeat finding program Piler [19].”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “There are a number of tools designed to automate TE identification and/or annotation, such as RECON [14], RepeatScout [15], PILER [16], RepeatModeler [17], Dfam [18], REPCLASS [19], REPET [20], and PASTEC [21], with none having distinct advantages [20, 22].”
Genome sequence of the cultivated cotton Gossypium arboreum (2014, neutral): “We used four software programs, LTR_FINDER 44 , PILER 45 , RepeatModeler and RepeatScout 46 , to generate the de novo repeat library.”
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome (2011, background): “, [20,22,27,28,29,30,31,32]), and are based on a diverse set of approaches (see [33,34] for reviews).”
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons (2008, methodology): “REPuter [5] (or the improved and more general software tool Vmatch [6]), RECON [7], RAP [8] and PILER [9].”