Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Roman R. Stocsits, Harald Letsch, Jana Hertel, Bernhard Misof , Peter F. Stadler
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Status: Published
Nucleic Acids Res. 2009 Oct;37(18):6184-93.
Abstract
Ribosomal RNA genes are probably the most frequently used data source in phylogenetic
reconstruction. Individual columns of rRNA alignments are not independent
as a consequence of their highly conserved secondary structures. Unless explicitly
taken into account, these correlation can distort the phylogenetic signal and/or
lead to gross overestimates of tree stability. Maximum Likelihood and Bayesian approaches
are of course amenable to using RNA-specific substitution models that
treat conserved base pairs appropriately, but require accurate secondary structure
models as input. So far, however, no accurate and easy-to-use tool has been available
for computing structure-aware aligments and consensus structures that can
deal with the large ribosomal RNAs. The RNAsalsa approach is designed to fill this
gap. Capitalizing on the improved accuracy of pairwise consensus structures and
informed by a priori knowledge of group-specific structural constraints, the tool
provides both alignments and consensus structures that are of sufficient accuracy
for routine phylogenetic analysis based on RNA-specific substitution models. The
power of the approach is demonstrated using two rRNA datasets: a mitochondrial
rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of
the five major echinoderm groups.
Keywords
alignment, RNA, secondary structure, phylogeny, evolution