Automated de novo identification of repeat sequence families in sequenced genomes.

By Z. Bao, Sean R. Eddy. Genome Research, 2002

936 citations recorded by the source corpus.

Repetitive sequences make up a major part of eukaryotic genomes. We have developed an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. When tested on the human genome, our approach was able to properly identify and group known transposable elements. The program, should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/466c8868c0e010d014706cc6401fb1a740f0e2d8

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Citations in the corpus

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].”
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. (2006, background): “, 2005) and the other generated by the de novo repeat mining program RECON (Bao and Eddy, 2002) (Z.”
FastPCR Software for PCR Primer and Probe Design and Repeat Search (2009, background): “There are many papers describing algorithms for finding repeats in a string; in most cases, alignment methods for finding repeats start with a self-comparison to detect repeated sequences (Kurtz, 2000; Kurtz et al. 2001; Bao and Eddy 2002; Lefebvre et al. 2003; Campagna et al. 2005; Edgar and Myers ”
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005, methodology): “%) to detect Release 3.1 TE annotations, but that RECON gave the best performance to recover Release 3.1 TEs exactly.”
Conservation and divergence of methylation patterning in plants and animals (2010, methodology): “Dispersed repeats for honey bee were identified de novo using the software RECON (10, 37).”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “briggsae, we applied RECON, an ab initio repetitive element identification algorithm (Bao and Eddy 2002) to identify repetitive sequences with more than ten copies in the genome.”
RepeatModeler2: automated genomic discovery of transposable element families (2019, methodology): “The RepeatScout and RECON analysis rounds reduce redundancy by masking out previously identified families with each . iteration.”
WindowMasker: window-based masker for sequenced genomes (2006, methodology): “Unlike RM, RECON compares the Ã To whom correspondence should be addressed.”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “At GIRI, TE identification mostly involves multiple rounds of running a homemade pipeline based on RECON [14].”
The Dfam database of repetitive DNA families (2015, methodology): “(1) continue the protocol used here to build alignments and profile HMMs from the Repbase-derived RepeatMasker library, which contains consensus sequences for TEs from dozens of organisms; (2) build curation assistance tools to enable straightforward external contribution of families to the openacce”
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).”
Genome Structure of the Legume, Lotus japonicus (2008, methodology): “Repetitive elements in the TGS were identified by comparing all of the contig units, HGS and those produced from the STM and SGRs, each using BLASTN(14,15) and processing the outputs using the RECON program.(16) A total of 214 consensus sequences of repetitive elements that appeared at least 20 time”
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, background): “The similarity of repeats in a genome is typically defined by percent identity from a pairwise alignment of the two sequences [30].”
RepeatModeler2 for automated genomic discovery of transposable element families (2020, methodology): “The RepeatScout and RECON analysis rounds reduce redundancy by masking out previously identifiedfamilieswitheachiteration.”
Assembly of long, error-prone reads using repeat graphs (2018, background): “This pair-wise representation is limited since it does not contribute to solving the repeat characterization problem 12,16 .”