Jul 21, 2016

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Algorithms for Molecular Biology : AMB
Timo Beller, Enno Ohlebusch

Abstract

Recently, Marcus et al. (Bioinformatics 30:3476-83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an [Formula: see text] time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Baier et al. (Bioinformatics 32:497-504, 2016) improved their result. In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele-a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.

  • References7
  • Citations3

References

  • References7
  • Citations3

Mentioned in this Paper

Genome
Genes
Trees (plant)
Bio-Informatics
Mathematical Formula
Comparative Genomic Analysis
Genes, vif
Graph Layout
Species
Alleles

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