POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria

  • Nicolas Wieseke
  • Marcus Lechner
  • Marcus Ludwig
  • Manja Marz
Conference paper

DOI: 10.1007/978-3-642-38036-5_25

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7875)
Cite this paper as:
Wieseke N., Lechner M., Ludwig M., Marz M. (2013) POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria. In: Cai Z., Eulenstein O., Janies D., Schwartz D. (eds) Bioinformatics Research and Applications. ISBRA 2013. Lecture Notes in Computer Science, vol 7875. Springer, Berlin, Heidelberg

Abstract

Multiple Genome-wide Alignments are a first crucial step to compare genomes. Gain and loss of genes, duplications and genomic rearrangements are challenging problems that aggravate with increasing phylogenetic distances. We describe a multiple genome-wide alignment tool for bacteria, called POMAGO, which is based on orthologous genes and their syntenic information determined by Proteinortho.This strategy enables POMAGO to efficiently define anchor points even across wide phylogenetic distances and outperform existing approaches in this field of application. The given set of orthologous genes is enhanced by several cleaning and completion steps, including the addition of previously undetected orthologous genes. Protein-coding genes are aligned on nucleotide and protein level, whereas intergenic regions are aligned on nucleotide level only. We tested and compared our program at three very different sets of bacteria that exhibit different degrees of phylogenetic distances: 1) 15 closely related, well examined and described E. coli species, 2) six more divergent Aquificales, as putative basal bacteria, and 3) a set of eight extreme divergent species, distributed among the whole phylogenetic tree of bacteria. POMAGO is written in a modular way which allows extending or even exchanging algorithms in different stages of the alignment process. Intergenic regions might for instance be aligned using an RNA secondary structure aware algorithm rather than to rely on sequence data alone. The software is freely available from http://www.rna.uni-jena.de/supplements/pomago

Keywords

Multiple Genome Alignment Synteny Annotation 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Nicolas Wieseke
    • 1
  • Marcus Lechner
    • 2
  • Marcus Ludwig
    • 3
  • Manja Marz
    • 3
  1. 1.Faculty of Mathematics and Computer ScienceUniversity of LeipzigLeipzigGermany
  2. 2.Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarburgGermany
  3. 3.Faculty of Mathematics and Computer ScienceFriedrich-Schiller-University JenaJenaGermany

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