ArticlePloS one2013
Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 16 citations in OpenAlex.
- Estimating Total Quantitative Protein Content inInternational journal of molecular sciences · 2023Article
- Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote.Plant & cell physiology · 2021Review
- Comparative Genomics Supports That Brazilian BioethanolFrontiers in microbiology · 2021Article
- Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast.Genetics · 2019Article
- The Transcription Factor ZafA Regulates the Homeostatic and Adaptive Response to Zinc Starvation inGenes · 2018Article
- Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae.Applied and environmental microbiology · 2018Article
- Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe.PloS one · 2016Article
- Article
- Defining the divergent enzymatic properties of RNA polymerases I and II.The Journal of biological chemistryArticle
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.