CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine

Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of transcripts are generated by large-scale cDNA and EST sequencing projects every year, there is a need for automatic methods to distinguish protein-coding RNAs from noncoding RNAs accurately and quickly. We developed a support vector machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC…

• CP
  China Postdoctoral Science Foundation
• HE
  Higher Education Discipline Innovation Project
• NH
  National High-tech Research and Development Program
• NK
  National Key Research and Development Program of China