RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits |
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Authors: | Hanno Teeling and Oliver Frank Gloeckner |
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Institution: | (1) Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany;(2) International University Bremen, D-28759 Bremen, Germany |
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Abstract: | Background Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic
relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based
trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of
complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers
and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods
that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which
has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences
nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs,
RibAlign has been developed to fill this gap. |
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Keywords: | |
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