RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

摘要: With the availability of genome-wide transcription data and massive comparative sequencing, discrimination coding from noncoding RNAs assessment potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, program to detect multiple sequence alignments that is optimized for emerging applications not covered by current protein gene finding software. Our algorithm combines information nucleotide substitution gap patterns unified framework also deals with real-life issues such alignment sequencing errors. It uses an explicit statistical model no machine learning component can therefore be applied “out box”, without any training, all domains life. We describe RNAcode method, apply it combination mass spectrometry experiments predict confirm seven novel short peptides E. coli analyze previously annotated “noncoding”. open source software available major platforms at http://wash.github.com/rnacode.