Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.

BMC Bioinformatics
Petr NovákJirí Macas

Abstract

The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization. We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, stati...Continue Reading

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Citations

Aug 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mateusz JanickiGuojun Yang
Oct 12, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Laura J Kelly, Ilia J Leitch
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Oct 31, 2013·Genome Génome / Conseil National De Recherches Canada·Kate L Hertweck
Jun 28, 2012·PLoS Genetics·Pavel NeumannJiří Macas
Jun 17, 2014·PloS One·Petr NovákJiří Macas
Feb 6, 2014·Genome Biology and Evolution·Laurent ModoloEmmanuelle Lerat
Mar 29, 2014·Genome Biology and Evolution·Elena BarghiniAndrea Cavallini
Jun 5, 2014·Bioinformatics·Matthias ZytnickiHadi Quesneville
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Sep 4, 2015·BMC Bioinformatics·Hamid YounesySteven Jm Jones

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Datasets Mentioned

BETA
AC235175
AC235457

Methods Mentioned

BETA
454 sequencing

Software Mentioned

cap3
Debian Linux
Tclust
RepeatMasker
R script
BioPerl
mgblast
blastx
blastn
igraph

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