POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions

• Published in: Bioinformatics 2007-08, Vol.23 (16), p.2046-2053
• Main Authors: Hirose, Shuichi, Shimizu, Kana, Kanai, Satoru, Kuroda, Yutaka, Noguchi, Tamotsu
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acid Sequence; Artificial Intelligence; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Chemical; Molecular Sequence Data; Pattern Recognition, Automated - methods; Protein Folding; Protein Structure, Tertiary; Proteins - chemistry; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment - methods; Sequence Analysis, Protein - methods
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btm302

Motivation: Recent experimental and theoretical studies have revealed several proteins containing sequence segments that are unfolded under physiological conditions. These segments are called disordered regions. They are actively investigated because of their possible involvement in various biological processes, such as cell signaling, transcriptional and translational regulation. Additionally, disordered regions can represent a major obstacle to high-throughput proteome analysis and often need to be removed from experimental targets. The accurate prediction of long disordered regions is thus expected to provide annotations that are useful for a wide range of applications. Results: We developed Prediction Of Order and Disorder by machine LEarning (POODLE-L; L stands for long), the Support Vector Machines (SVMs) based method for predicting long disordered regions using 10 kinds of simple physico-chemical properties of amino acid. POODLE-L assembles the output of 10 two-level SVM predictors into a final prediction of disordered regions. The performance of POODLE-L for predicting long disordered regions, which exhibited a Matthew's correlation coefficient of 0.658, was the highest when compared with eight well-established publicly available disordered region predictors. Availability: POODLE-L is freely available at http://mbs.cbrc.jp/poodle/poodle-l.html Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.