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.
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) 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.
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data
Stefan Washietl, Sven Findeiß Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß, Nick Goldman
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Status: Published
RNA 2011 Apr;17(4):578-594
Abstract
Evolutionary analysis has become an powerful tool for the functional annotation of genomes
due to the availability of massive amounts of comparative sequence data. The assessment
of coding potential in conserved regions and the discrimination of coding from
noncoding transcripts arose as a core analysis task. Here we present RNAcode, a program
to detect coding regions in multiple sequence alignments that is optimized for emerging
applications not covered by current gene finding software. Our algorithm combines information
from nucleotide substitution and gap patterns in a unified framework and also
deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical
model with no machine learning component and can therefore be applied “out of
the box”, without any training, to data from all domains of life. We describe the RNAcode
method, and apply it in combination with mass spectrometry experiments to predict and
confirm seven novel short peptides in E. coli and to analyze the coding potential of RNAs
previously annotated as “noncoding”. RNAcode is open source software and available for
all major platforms at http://wash.github.com/rnacode.
Keywords
coding sequence, comparative genomics, RNAcode, peptides