Dataset Information

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

ABSTRACT: Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery of large and 'hidden' transcriptome rejuvenates the demand for methods that can rapidly distinguish between coding and noncoding RNA. Here, we present a novel alignment-free method, Coding Potential Assessment Tool (CPAT), which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. To this end, CPAT uses a logistic regression model built with four sequence features: open reading frame size, open reading frame coverage, Fickett TESTCODE statistic and hexamer usage bias. CPAT software outperformed (sensitivity: 0.96, specificity: 0.97) other state-of-the-art alignment-based software such as Coding-Potential Calculator (sensitivity: 0.99, specificity: 0.74) and Phylo Codon Substitution Frequencies (sensitivity: 0.90, specificity: 0.63). In addition to high accuracy, CPAT is approximately four orders of magnitude faster than Coding-Potential Calculator and Phylo Codon Substitution Frequencies, enabling its users to process thousands of transcripts within seconds. The software accepts input sequences in either FASTA- or BED-formatted data files. We also developed a web interface for CPAT that allows users to submit sequences and receive the prediction results almost instantly.

SUBMITTER: Wang L

PROVIDER: S-EPMC3616698 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Publications

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Wang Liguo L Park Hyun Jung HJ Dasari Surendra S Wang Shengqin S Kocher Jean-Pierre JP Li Wei W

Nucleic acids research 20130117 6

Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery of large and 'hidden' transcriptome rejuvenates the demand for methods that can rapidly distinguish between coding and noncoding RNA. Here, we present a novel alignment-free method, Coding Potential Assessment Tool (CPAT), which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. To this end, CPAT uses a logistic regression model built with four sequence featur ...[more]

PMID: 23335781

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Dataset Information

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Publications

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Similar Datasets

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