distinguishing protein-coding from non-coding rnas through support vector machines通过支持向量机区分蛋白质编码和非编码rna.pdfVIP

Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines 1,2,3* 4 1,2,3 Jinfeng Liu , Julian Gough , Burkhard Rost 1 Columbia University Bioinformatics Center, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America, 2 Columbia University Center for Computational Biology and Bioinformatics, New York, New York, United States of America, 3 Northeast Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America, 4 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan RIKEN’s FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in general. Increasing evidence points to the important cellular roles of such non-coding RNAs (ncRNAs). The distinction of protein-coding RNA transcripts from ncRNA transcripts is therefore an important problem in understanding the transcriptome and carrying out its annotation. Very few in silico methods have specifically addressed this problem. Here, we introduce CONC (for ‘‘coding or non-coding’’), a novel method based on support vector machines that classifies transcripts according to features they would have if they were coding for proteins. These features include peptide length, amino acid composition, predicted secondary structure content, predicted percentage of exposed residues, compositional entropy, number of homologs from database searches, and