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

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 biologic...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Bioinformatics 2007-08, Vol.23 (16), p.2046-2053
Hauptverfasser: Hirose, Shuichi, Shimizu, Kana, Kanai, Satoru, Kuroda, Yutaka, Noguchi, Tamotsu
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext bestellen
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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: hirose-shuichi@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btm302