原创力文档a combination of compositional index and genetic algorithm for predicting transmembrane helical segments的组合成分指数和遗传算法预测跨膜螺旋段.pdfVIP
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a combination of compositional index and genetic algorithm for predicting transmembrane helical segments的组合成分指数和遗传算法预测跨膜螺旋段
A Combination of Compositional Index and Genetic
Algorithm for Predicting Transmembrane Helical
Segments
1 2 1
Nazar Zaki *, Salah Bouktif , Sanja Lazarova-Molnar
1 Intelligent Systems, Faculty of Information Technology, United Arab Emirates (UAE) University, Al-Ain, United Arab Emirates, 2 Software Development, Faculty of
Information Technology, United Arab Emirates (UAE) University, Al-Ain, United Arab Emirates
Abstract
Transmembrane helix (TMH) topology prediction is becoming a focal problem in bioinformatics because the structure of TM
proteins is difficult to determine using experimental methods. Therefore, methods that can computationally predict the
topology of helical membrane proteins are highly desirable. In this paper we introduce TMHindex, a method for detecting
TMH segments using only the amino acid sequence information. Each amino acid in a protein sequence is represented by a
Compositional Index, which is deduced from a combination of the difference in amino acid occurrences in TMH and non-
TMH segments in training protein sequences and the amino acid composition information. Furthermore, a genetic
algorithm was employed to find the optimal threshold value for the separation of TMH segments from non-TMH segments.
The method successfully predicted 376 out of the 378 TMH segments in a dataset consisting of 70 test protein sequences.
The sensitivity and specificity for classifying each amino acid in every protein sequence in the dataset was 0.901 and 0.865,
respectively. To assess the generality of TMHindex, we also tested the approach on another standard 73-protein 3D helix
dataset. TMHindex correctly predicted 91.8% of proteins based on TM segments. The level of the accuracy achieved using
TMHindex in comparison to other r
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