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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Project description:In order to understand consumer perception, reduce risks in online shopping, and maintain online security, this study employs data envelopment analysis (DEA) to confirm the relationship between evaluation and stimuli. It establishes a model of stimuli-organism response and uses regression analysis to explore the relationships among negative online shopping evaluations, consumer perception of risk, and consumer behavior. This study employs attribution theory to analyze the impact of evaluations on consumer behavior and assesses the role of perceived risk as a mediator. The independent variable is negative comments, the dependent variable is consumer behavior, and logistic regression is used to empirically analyze the factors influencing online shopping security. The results indicate a positive correlation between the number of negative comments and consumers' delayed purchase behavior, with a correlation coefficient of 41%. The intensity of negative comments significantly impacts consumers' refusal to make a purchase, with a correlation coefficient of 38%. The length of negative comments substantially influences consumers' opposition to purchasing, also with a correlation coefficient of 38%. There is a close relationship between perceived risk and consumers' delayed shopping behavior and the number of negative comments, with 41% and 4% correlation coefficients, respectively. Perceived risk has a relatively smaller impact on consumers' opposition to purchase behavior, with a correlation coefficient of 27%. The length, intensity, and number of negative comments are correlated with consumers' opposition, refusal, and delayed consumption, negatively affecting consumer intent. Additionally, negative comments are related to perceived risk and consumer behavior. Perceived risk causally influences consumer behavior, while the convenience of shopping has a relatively minor impact on online shopping security. Factors like delivery speed, buyer reviews, brand, price, and consumer perception are significantly related to online shopping security. Consumer perception has the most significant impact on online shopping security, balancing secure and fast consumption under the guarantee of user experience. Strengthening consumer perception enhances consumers' ability to process risk information, helping them better identify risks and avoid using hazardous network software, tools, or technologies, thereby reducing potential online security risks.

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.

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