title: Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines.
abstract: The annotation of the well-studied organism, Saccharomyces cerevisiae, has been improving over the past decade while there are unresolved debates over the amount of biologically significant open reading frames (ORFs) in yeast genome. We revisited the total count of protein-coding genes in S. cerevisiae S288c genome using a theoretical approach by combining the Support Vector Machine (SVM) method with six widely used measurements of sequence statistical features. The accuracy of our method is over 99.5% in 10-fold cross-validation. Based on the annotation data in Saccharomyces Genome Database (SGD), we studied the coding capacity of all 1744 ORFs which lack experimental results and suggested that the overall number of chromosomal ORFs encoding proteins in yeast should be 6091 by removing 488 spurious ORFs. The importance of the present work lies in at least two aspects. First, cross-validation and retrospective examination showed the fidelity of our method in recognizing ORFs that likely encode proteins. Second, we have provided a web service that can be accessed at http://cobi.uestc.edu.cn/services/yeast/, which enables the prediction of protein-coding ORFs of the genus Saccharomyces with a high accuracy.
authors.affiliation: Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Lin
authors.forename: Xin
authors.initials: X
authors.lastname: Yin
authors.forename: Xianlong
authors.initials: X
authors.lastname: Wang
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D002138:Calibration; D019295:Computational Biology / Q000379:methods / Q000592:standards; D005800:Genes, Fungal; D016681:Genome, Fungal / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods* / Q000592:standards; D015999:Multivariate Analysis; D016366:Open Reading Frames / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D060388:Support Vector Machine
chemical_list: D029701:Saccharomyces cerevisiae Proteins