Linearization of genome sequence graphs revisited

iScience

Anna Lisiecka¹  Norbert Dojer¹ 

[1] Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland;

关键词: Bioinformatics;    Computer science;    Genomics;   

DOI  :  

来源: DOAJ

【 摘 要 】

Summary: The need to include the genetic variation within a population into a reference genome led to the concept of a genome sequence graph. Nodes of such a graph are labeled with DNA sequences occurring in represented genomes. Due to double-stranded nature of DNA, each node may be oriented in one of two possible ways, resulting in marking one end of the labeling sequence as in-side and the other as out-side. Edges join pairs of sides and reflect adjacency between node sequences in genomes constituting the graph. Linearization of a sequence graph aims at orienting and ordering graph nodes in a way that makes it more efficient for visualization and further analysis, e.g. access and traversal. We propose a new linearization algorithm, called ALIBI – Algorithm for Linearization by Incremental graph BuIlding. The evaluation shows that ALIBI is computationally very efficient and generates high-quality results.

【 授权许可】

Unknown