Abstract:
BACKGROUND:The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently. RESULTS:This work focuses on providing a tool for discovering and visualizing the relationships between the sequences constituting a pan-genome. A new structure to represent such relationships - called affinity tree - is proposed. Each node of this tree has assigned a subset of genomes, as well as their homogeneity level and averaged consensus sequence. Moreover, subsets assigned to sibling nodes form a partition of the genomes assigned to their parent. CONCLUSIONS:Functionality of affinity tree is demonstrated on simulated data and on the Ebola virus pan-genome. Furthermore, two software packages are provided: PangTreeBuild constructs affinity tree, while PangTreeVis presents its result.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Dziadkiewicz P,Dojer Ndoi
10.1186/s12864-020-6610-4subject
Has Abstractpub_date
2020-04-16 00:00:00pages
274issue
Suppl 2issn
1471-2164pii
10.1186/s12864-020-6610-4journal_volume
21pub_type
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