Evolutionary Bioinformatics Online最新文献_第4页

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data NABIC:一个搜索、可视化和共享农业基因组学数据的新入口

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S34493

Y. Seol, Tae-Ho Lee, Dong-Suk Park, Chang-Kug Kim

引用次数: 11

Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups 谷胱甘肽s -转移酶基因Phi类在非植物类群中广泛存在

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S35909

Jean-Pierre Munyampundu, You-ping Xu, Xin-Zhong Cai

{"title":"Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups","authors":"Jean-Pierre Munyampundu, You-ping Xu, Xin-Zhong Cai","doi":"10.4137/EBO.S35909","DOIUrl":"https://doi.org/10.4137/EBO.S35909","url":null,"abstract":"Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122435653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Prefiltering Model for Homology Detection Algorithms on GPU GPU上同调检测算法的预滤波模型

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40877

Germán Retamosa, L. de Pedro, Iván González, J. Tamames

{"title":"Prefiltering Model for Homology Detection Algorithms on GPU","authors":"Germán Retamosa, L. de Pedro, Iván González, J. Tamames","doi":"10.4137/EBO.S40877","DOIUrl":"https://doi.org/10.4137/EBO.S40877","url":null,"abstract":"Homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. However, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. Thus, their acceleration is essential. The aim of this article was to prefilter a sequence database. To make this work, we have implemented a groundbreaking heuristic model based on NVIDIA's graphics processing units (GPUs) and multicore processors. Depending on the sensitivity settings, this makes it possible to quickly reduce the sequence database by factors between 50% and 95%, while rejecting no significant sequences. Furthermore, this prefiltering application can be used together with multiple homology detection algorithms as a part of a next-generation sequencing system. Extensive performance and accuracy tests have been carried out in the Spanish National Centre for Biotechnology (NCB). The results show that GPU hardware can accelerate the execution times of former homology detection applications, such as National Centre for Biotechnology Information (NCBI), Basic Local Alignment Search Tool for Proteins (BLASTP), up to a factor of 4. KEY POINTS • Owing to the increasing size of the current sequence datasets, filtering approach and high-performance computing (HPC) techniques are the best solution to process all these information in acceptable processing times. • Graphics processing unit cards and their corresponding programming models are good options to carry out these processing methods. • Combination of filtration models with HPC techniques is able to offer new levels of performance and accuracy in homology detection algorithms such as National Centre for Biotechnology Information Basic Local Alignment Search Tool.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115888529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization 当前细菌基因编码胶囊生物合成蛋白CapI包含由外显子化衍生的核苷酸

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40703

Yong Wang, Xia-Fang Tao, Zhixi Su, Ake Liu, Tian-Lei Liu, Ling Sun, Q. Yao, Ke-ping Chen, X. Gu

{"title":"Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization","authors":"Yong Wang, Xia-Fang Tao, Zhixi Su, Ake Liu, Tian-Lei Liu, Ling Sun, Q. Yao, Ke-ping Chen, X. Gu","doi":"10.4137/EBO.S40703","DOIUrl":"https://doi.org/10.4137/EBO.S40703","url":null,"abstract":"Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5'-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5'-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127081537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS 用msParSm作为MaCS的替代方法来接近长基因组区域和大重组率

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40268

Carlos Montemuiño, Antonio Espinosa, J. Moure, Gonzalo Vera, P. Hernández, S. Ramos-Onsins

引用次数: 0

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching 使用模式匹配检测重复嵌套基序的生物信息学方法

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40138

J. R. Romero, J. A. Carballido, I. Garbus, V. Echenique, I. Ponzoni

引用次数: 1

EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers EvalMSA:一个程序来评估多个序列比对和检测异常值

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40583

Á. Chiner-Oms, F. González-Candelas

引用次数: 8

Genome-Wide Analysis of NBS-LRR Genes in Sorghum Genome Revealed Several Events Contributing to NBS-LRR Gene Evolution in Grass Species 高粱NBS-LRR基因的全基因组分析揭示了牧草NBS-LRR基因进化的几个事件

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S36433

Xiping Yang, Jianping Wang

引用次数: 37

Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82 艰难梭菌ZJCDC-S82基因组序列分析

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S32476

Yun Luo, Chen Huang, Ju-lian Ye, W. Fang, W. Gu, Zhi-ping Chen, Hui Li, Xianjun Wang, Dazhi Jin

{"title":"Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82","authors":"Yun Luo, Chen Huang, Ju-lian Ye, W. Fang, W. Gu, Zhi-ping Chen, Hui Li, Xianjun Wang, Dazhi Jin","doi":"10.4137/EBO.S32476","DOIUrl":"https://doi.org/10.4137/EBO.S32476","url":null,"abstract":"Peptoclostridium difficile (Clostridium difficile) is the major pathogen associated with infectious diarrhea in humans. Concomitant with the increased incidence of C. difficile infection worldwide, there is an increasing concern regarding this infection type. This study reports a draft assembly and detailed sequence analysis of C. difficile strain ZJCDC-S82. The de novo assembled genome was 4.19 Mb in size, which includes 4,013 protein-coding genes, 41 rRNA genes, and 84 tRNA genes. Along with the nuclear genome, we also assembled sequencing information for a single plasmid consisting of 11,930 nucleotides. Comparative genomic analysis of C. difficile ZJCDC-S82 and two other previously published strains, such as M120 and CD630, showed extensive similarity. Phylogenetic analysis revealed that genetic diversity among C. difficile strains was not influenced by geographic location. Evolutionary analysis suggested that four genes encoding surface proteins exhibited positive selection in C. difficile ZJCDC-S82. Codon usage analysis indicated that C. difficile ZJCDC-S82 had high codon usage bias toward A/U-ended codons. Furthermore, codon usage patterns in C. difficile ZJCDC-S82 were predominantly affected by mutation pressure. Our results provide detailed information pertaining to the C. difficile genome associated with a strain from mainland China. This analysis will facilitate the understanding of genomic diversity and evolution of C. difficile strains in this region.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130134486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment IBBOMSA:一种基于生物地理学的多序列比对改进方法

Evolutionary Bioinformatics Online Pub Date : 2016-01-01 DOI: 10.4137/EBO.S40457

R. Yadav, H. Banka

引用次数: 6