Prediction of Sphingosine protein-coding regions with a self adaptive spectral rotation method

• Published in: PloS one Vol. 14; no. 4; p. e0214442
• Main Authors: Li, Zhongwei, Guan, Yanan, Yuan, Xiang, Zheng, Pan, Zhu, Hu
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 03.04.2019; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Artificial intelligence; Bioinformatics; Biology; Biology and Life Sciences; Communication; Computer and Information Sciences; Computer applications; Computer simulation; Concrete; Concrete construction; Construction industry; Construction Materials; Data processing; Databases, Genetic; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Bacterial - genetics; Engineering; Fermentation; Fragmentation; Fragments; Gene sequencing; Genes; Genome, Bacterial; Genomes; Genomics; Identification methods; Markov processes; Metabolism; Methods; Neural networks; Nucleotide sequence; Oil recovery; Open Reading Frames; Periodicity; Petroleum engineering; Petroleum mining; Physical Sciences; Polysaccharides, Bacterial - biosynthesis; Predictions; Proteins; Research and Analysis Methods; Researchers; Rotation; Sphingomonas; Sphingomonas - genetics; Sphingosine; Sphingosine - chemistry; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0214442

Identifying protein coding regions in DNA sequences by computational methods is an active research topic. Welan gum produced by Sphingomonas sp. WG has great application potential in oil recovery and concrete construction industry. Predicting the coding regions in the Sphingomonas sp. WG genome and addressing the mechanism underlying the explanation for the synthesis of Welan gum metabolism is an important issue at present. In this study, we apply a self adaptive spectral rotation (SASR, for short) method, which is based on the investigation of the Triplet Periodicity property, to predict the coding regions of the whole-genome data of Sphingomonas sp. WG without any previous training process, and 1115 suspected gene fragments are obtained. Suspected gene fragments are subjected to a similarity search against the non-redundant protein sequences (nr) database of NCBI with blastx, and 762 suspected gene fragments have been labeled as genes in the nr database.