Details zur Publikation

Referenztyp Zeitschriften
DOI / URL Link
Titel (primär) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data
Autor Washietl, S.; Findeiss, S.; Müller, S.A.; Kalkhof, S.; von Bergen, M.; Hofacker, I.L.; Stadler, P.F.; Goldmann, N.
Journal / Serie RNA : a publication of the RNA Society
Erscheinungsjahr 2011
Department PROTEOM
Band/Volume 17
Heft 4
Seite von 578
Seite bis 594
Sprache englisch
Abstract

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions 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 protein 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 Escherichia 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.

dauerhafte UFZ-Verlinkung https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=11144
Washietl, S., Findeiss, S., Müller, S.A., Kalkhof, S., von Bergen, M., Hofacker, I.L., Stadler, P.F., Goldmann, N. (2011):
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data
RNA 17 (4), 578 - 594