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

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...

Full description

Saved in:
Bibliographic Details
Published in:PloS one 2019-04, Vol.14 (4), p.e0214442-e0214442
Main Authors: Li, Zhongwei, Guan, Yanan, Yuan, Xiang, Zheng, Pan, Zhu, Hu
Format: Article
Language:English
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
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0214442