title: iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition.
abstract: Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called "iTIS-PseTNC," was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method.
authors.affiliation: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China; Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address: chenweiimu@gmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: School of Public Health, Hebei United University, Tangshan 063000, China. Electronic address: fengpengmian@gmail.com.
authors.forename: Peng-Mian
authors.initials: PM
authors.lastname: Feng
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: enzeas@gmail.com.
authors.forename: En-Ze
authors.initials: EZ
authors.lastname: Deng
authors.affiliation: Gordon Life Science Institute, Boston, MA 02478, USA; Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: hlin@uestc.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
authors.affiliation: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China; Gordon Life Science Institute, Boston, MA 02478, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: kcchou@gordonlifescience.org.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015894:Genome, Human / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D009841:Oligonucleotides / Q000235:genetics*; D010442:Peptide Chain Initiation, Translational; D060388:Support Vector Machine; D014584:User-Computer Interface
chemical_list: D009841:Oligonucleotides
keywords: Physicochemical properties; Pseudo trinucleotide composition; Support vector machine; Translation initiation site; Web server; iTIS-PseTNC