期刊
RNA
卷 17, 期 4, 页码 578-594出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.2536111
关键词
coding sequence; comparative genomics; small peptides; transcriptome
资金
- Wellcome Trust [078968]
- Deutsche Forschungsgemeinschaft [STA 850/7-1, SPP-1258]
- Austrian GEN-AU
- GEN-AU
- Bundesministerium fur Wissenschaft und Forschung
- Austrian Science Fund (FWF) [W1207] Funding Source: Austrian Science Fund (FWF)
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.
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