Performance
Analysis of Methods that Predict Transmembrane Regions
CHEN Zhong-Qiang*, LIU Qi, ZHU
Yi-Sheng, LI Yi-Xue1
( Department of Biomedical Engineering, Shanghai Jiaotong University,
Shanghai 200030, China; 1Bioinformation Center,
Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences,
Shanghai 200031, China )
Abstract
The increasing protein sequences from the genome project require the oretical
methods to predict transmembrane regions. Evaluation of these prediction
methods will not only help biologists to select appropriate methods, but also
provide bioinformatian guidance to develop new methods. In this work, the
latest membrane protein topology database was used as the test set and selected
soluble proteins was used as control.The analyses of performance of published
online prediction methods are presented. Results show that HMMTOP (2.0) has the
best performance among current methods.
Key words
membrane protein;transmembrane region;secondary structure prediction
*Corresponding author: Tel,
86-21-62932832-155; e-mail, [email protected]