License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/OASIcs.GCB.2013.35
URN: urn:nbn:de:0030-drops-42314
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Ernst, Corinna ; Rahmann, Sven

PanCake: A Data Structure for Pangenomes

p035-ernst.pdf (2 MB)


We present a pangenome data structure ("PanCake") for sets of related genomes, based on bundling similar sequence regions into shared features, which are derived from genome-wide pairwise sequence alignments.
We discuss the design of the data structure, basic operations on it and methods to predict core genomes and singleton regions.
In contrast to many other pangenome analysis tools, like EDGAR or PGAT, PanCake is independent of gene annotations.
Nevertheless, comparison of identified core and singleton regions shows good agreements.
The PanCake data structure requires significantly less space than the sum of individual sequence files.

BibTeX - Entry

  author =	{Corinna Ernst and Sven Rahmann},
  title =	{{PanCake: A Data Structure for Pangenomes}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{35--45},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Tim Bei{\ss}barth and Martin Kollmar and Andreas Leha and Burkhard Morgenstern and Anne-Kathrin Schultz and Stephan Waack and Edgar Wingender},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{},
  URN =		{urn:nbn:de:0030-drops-42314},
  doi =		{10.4230/OASIcs.GCB.2013.35},
  annote =	{Keywords: pangenome, data structure, core genome, comparative genomics}

Keywords: pangenome, data structure, core genome, comparative genomics
Collection: German Conference on Bioinformatics 2013
Issue Date: 2013
Date of publication: 09.09.2013

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