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DOI: 10.4230/OASIcs.GCB.2013.35

PanCake: A Data Structure for Pangenomes

Authors: Corinna Ernst and Sven Rahmann

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract

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.

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Corinna Ernst and Sven Rahmann. PanCake: A Data Structure for Pangenomes. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 35-45, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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

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PanCake: A Data Structure for Pangenomes

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