iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition.

Wei Chen, Peng-Mian Feng, En-Ze Deng, Hao Lin, Kuo-Chen Chou

Journal: Analytical biochemistry 2015;462():76-83

PMID: 25016190

Full Text on Elsevier Science View on PubMed

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.

Address: 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: [email protected].; School of Public Health, Hebei United University, Tangshan 063000, China. Electronic address: [email protected].; 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: [email protected].; 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: [email protected].; 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: [email protected].

DOI: 10.1016/j.ab.2014.06.022

Link outs

Free resources

Other Literature Sources:

https://scite.ai/reports/25016190

Research Materials:

https://antibodies.cancer.gov/detail/CPTC-HLA-B-1

Subscription / membership required

Full Text Sources:

https://linkinghub.elsevier.com/retrieve/pii/S0003...

MeSH Terms: Algorithms, Base Sequence, Genome, Human, Genomics, Humans, Internet, Oligonucleotides, Peptide Chain Initiation, Translational, Support Vector Machine, User-Computer Interface