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Pesquisa : G05.360.340.358 [Categoria DeCS]
Referências encontradas : 119 [refinar]
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[PMID]:28451978
[Au] Autor:Uchiyama I
[Ad] Endereço:Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan. uchiyama@nibb.ac.jp.
[Ti] Título:Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.
[So] Source:Methods Mol Biol;1611:147-168, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a "My MBGD" mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.
[Mh] Termos MeSH primário: Genoma Microbiano/genética
Software
[Mh] Termos MeSH secundário: Algoritmos
Bases de Dados Genéticas
Genômica
Filogenia
Alinhamento de Sequência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_12


  2 / 119 MEDLINE  
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[PMID]:28449639
[Au] Autor:Agrawal S; Arze C; Adkins RS; Crabtree J; Riley D; Vangala M; Galens K; Fraser CM; Tettelin H; White O; Angiuoli SV; Mahurkar A; Fricke WF
[Ad] Endereço:Institute for Genome Sciences, Baltimore, MD, USA.
[Ti] Título:CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.
[So] Source:BMC Genomics;18(1):332, 2017 04 27.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CONCLUSIONS: CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.
[Mh] Termos MeSH primário: Computação em Nuvem
Genômica/métodos
Software
[Mh] Termos MeSH secundário: Automação
Genoma Microbiano/genética
Alinhamento de Sequência
Análise de Sequência
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, P.H.S.
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180104
[Lr] Data última revisão:
180104
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-017-3717-3


  3 / 119 MEDLINE  
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[PMID]:28513710
[Au] Autor:Walsh CT
[Ad] Endereço:ChEM-H Center, Stanford University, Stanford, CA 94305, USA. cwalsh2@stanford.edu.
[Ti] Título:Are highly morphed peptide frameworks lurking silently in microbial genomes valuable as next generation antibiotic scaffolds?
[So] Source:Nat Prod Rep;34(7):687-693, 2017 Jul 01.
[Is] ISSN:1460-4752
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Antibiotics are a therapeutic class that, once deployed, select for resistant bacterial pathogens and so shorten their useful life cycles. As a consequence new versions of antibiotics are constantly needed. Among the antibiotic natural products, morphed peptide scaffolds, converting conformationally mobile, short-lived linear peptides into compact, rigidified small molecule frameworks, act on a wide range of bacterial targets. Advances in bacterial genome mining, biosynthetic gene cluster prediction and expression, and mass spectroscopic structure analysis suggests many more peptides, modified both in side chains and peptide backbones, await discovery. Such molecules may turn up new bacterial targets and be starting points for combinatorial or semisynthetic manipulations to optimize activity and pharmacology parameters.
[Mh] Termos MeSH primário: Antibacterianos/farmacologia
Produtos Biológicos/farmacologia
Genoma Microbiano
Peptídeos/farmacologia
[Mh] Termos MeSH secundário: Antibacterianos/química
Bactérias/metabolismo
Produtos Biológicos/química
Genoma Bacteriano
Estrutura Molecular
Família Multigênica
Peptídeos/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Biological Products); 0 (Peptides)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170809
[Lr] Data última revisão:
170809
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170518
[St] Status:MEDLINE
[do] DOI:10.1039/c7np00011a


  4 / 119 MEDLINE  
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[PMID]:28379490
[Au] Autor:Xia X
[Ad] Endereço:From the Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, ON K1N 6N5, Canada.
[Ti] Título:DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution.
[So] Source:J Hered;108(4):431-437, 2017 Jun 01.
[Is] ISSN:1465-7333
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon-anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain. Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for nonlinear clustering of transcriptomic data, comprehensive sequence alignment, and phylogenetic functions. DAMBE features a graphic, user-friendly and intuitive interface, and is freely available from http://dambe.bio.uottawa.ca.
[Mh] Termos MeSH primário: Evolução Molecular
Genoma Microbiano
Genômica/métodos
Filogenia
[Mh] Termos MeSH secundário: Algoritmos
Biologia Computacional
Elongação Traducional da Cadeia Peptídica
Iniciação Traducional da Cadeia Peptídica
Alinhamento de Sequência
Software
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170907
[Lr] Data última revisão:
170907
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170406
[St] Status:MEDLINE
[do] DOI:10.1093/jhered/esx033


  5 / 119 MEDLINE  
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[PMID]:28187207
[Au] Autor:Budinich M; Bourdon J; Larhlimi A; Eveillard D
[Ad] Endereço:Computational Biology group, LINA UMR 6241 CNRS, EMN, Université de Nantes, Nantes, France.
[Ti] Título:A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.
[So] Source:PLoS One;12(2):e0171744, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.
[Mh] Termos MeSH primário: Genoma Microbiano
Microbiota/genética
Modelos Teóricos
[Mh] Termos MeSH secundário: Fontes Termais/microbiologia
Redes e Vias Metabólicas
Microbiota/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170809
[Lr] Data última revisão:
170809
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170211
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0171744


  6 / 119 MEDLINE  
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[PMID]:28119518
[Au] Autor:Baltz RH
[Ad] Endereço:CognoGen Biotechnology Consulting, Sarasota, FL, USA.
[Ti] Título:Molecular beacons to identify gifted microbes for genome mining.
[So] Source:J Antibiot (Tokyo);70(5):639-646, 2017 May.
[Is] ISSN:0021-8820
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:Microbial genome mining is a promising technology that is revitalizing natural product discovery. It is now well documented that many bacteria with large genomes, particularly actinomycetes, encode many more secondary metabolites (SMs) than was previously known from their expressed secondary metabolomes. There are effective bioinformatics tools for counting the numbers and nature of SMs, and determining the total coding capacity from finished microbial genomes. However, these methods do not translate well to draft genomes, particularly for large SM gene clusters that contain nonribosomal peptide synthetase (NRPS) or type I polyketide synthase (PKS-I) mega-genes which are prone to fragmentation and misassembly. Small molecular beacons are required to assess the numbers and variety of NRPS, PKS-I and mixed NRPS/PKS-I pathways. In this report, I show that concatenated peptidyl carrier protein-thioesterase di-domains and acyl carrier protein-thioesterase di-domains can be used as multi-probes to survey finished or draft genomes to estimate the numbers of NRPS, PKS-I and mixed NRPS/PKS-I gene clusters to identify gifted actinomycetes.
[Mh] Termos MeSH primário: Actinobacteria/genética
Produtos Biológicos/isolamento & purificação
Mineração de Dados
Genoma Bacteriano
[Mh] Termos MeSH secundário: Actinobacteria/metabolismo
Descoberta de Drogas/métodos
Genoma Microbiano
Família Multigênica
Peptídeo Sintases/genética
Policetídeo Sintases/genética
Metabolismo Secundário
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biological Products); 79956-01-7 (Polyketide Synthases); EC 6.3.2.- (Peptide Synthases); EC 6.3.2.- (non-ribosomal peptide synthase)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170620
[Lr] Data última revisão:
170620
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170126
[St] Status:MEDLINE
[do] DOI:10.1038/ja.2017.1


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[PMID]:28111203
[Au] Autor:Manor O; Borenstein E
[Ad] Endereço:Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
[Ti] Título:Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.
[So] Source:Cell Host Microbe;21(2):254-267, 2017 Feb 08.
[Is] ISSN:1934-6069
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.
[Mh] Termos MeSH primário: Biologia Computacional
Microbiota
Software
[Mh] Termos MeSH secundário: Actinobacteria/classificação
Bacteroides/classificação
Doenças Transmissíveis/microbiologia
Bases de Dados Genéticas
Diabetes Mellitus Tipo 2/microbiologia
Firmicutes/classificação
Genoma Microbiano
Seres Humanos
Metagenômica
Filogenia
Proteobactérias/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170911
[Lr] Data última revisão:
170911
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170124
[St] Status:MEDLINE


  8 / 119 MEDLINE  
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[PMID]:27943013
[Au] Autor:Wang X; Xu X; Xia Y
[Ad] Endereço:BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. viruswater@hotmail.com.
[Ti] Título:Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus.
[So] Source:Antonie Van Leeuwenhoek;110(3):445-453, 2017 Mar.
[Is] ISSN:1572-9699
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:In recent years, metagenome-wide association studies have revealed potential relationships between intestinal microbiomes and the pathogenesis of type 2 diabetes mellitus (T2DM). However, considering the increase in volume of gene catalogues and algorithms, an updated analysis would be expected to confirm previous discoveries and provide new knowledge. We therefore constructed new profiles after mapping the recent catalogue of reference genes in the human gut microbiome to reanalyze samples from T2DM cases and controls in the Chinese population. We identified different compositions between Chinese controls and T2DM patients at the species and genus levels, especially in the case of butyrate-producing bacteria, Haemophilus, and Lactobacillus. An effective metagenomic linkage group random forest model was built to differentiate controls from T2DM cases in different cohorts. Functional markers from the Kyoto Encyclopedia of Genes and Genomes database were identified using new annotations. We also report 16 virulence factor markers and 22 antibiotic resistance markers associated with T2DM.
[Mh] Termos MeSH primário: Diabetes Mellitus Tipo 2/microbiologia
Microbioma Gastrointestinal/genética
[Mh] Termos MeSH secundário: China/epidemiologia
Estudos de Coortes
Diabetes Mellitus Tipo 2/epidemiologia
Fezes/microbiologia
Marcadores Genéticos/genética
Genoma Microbiano
Seres Humanos
Metagenoma
Metagenômica/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170328
[Lr] Data última revisão:
170328
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161213
[St] Status:MEDLINE
[do] DOI:10.1007/s10482-016-0805-3


  9 / 119 MEDLINE  
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[PMID]:27840430
[Au] Autor:Power RA; Parkhill J; de Oliveira T
[Ad] Endereço:Africa Centre for Population Health, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
[Ti] Título:Microbial genome-wide association studies: lessons from human GWAS.
[So] Source:Nat Rev Genet;18(1):41-50, 2017 01.
[Is] ISSN:1471-0064
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The reduced costs of sequencing have led to whole-genome sequences for a large number of microorganisms, enabling the application of microbial genome-wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS are likely to further advance our understanding of infectious diseases. These advances include insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this Review, we outline the methodologies of GWAS, the current state of the field of microbial GWAS, and how lessons from human GWAS can direct the future of the field.
[Mh] Termos MeSH primário: Doenças Transmissíveis/genética
Predisposição Genética para Doença
Genoma Humano
Genoma Microbiano
Estudo de Associação Genômica Ampla
[Mh] Termos MeSH secundário: Doenças Transmissíveis/microbiologia
Genótipo
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170512
[Lr] Data última revisão:
170512
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161115
[St] Status:MEDLINE
[do] DOI:10.1038/nrg.2016.132


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[PMID]:27610931
[Au] Autor:Wang Y; Hu H; Li X
[Ad] Endereço:1 Department of Computer Science, University of Central Florida , Orlando, Florida.
[Ti] Título:rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.
[So] Source:J Comput Biol;24(4):368-375, 2017 Apr.
[Is] ISSN:1557-8666
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Metatranscriptomics studies the transcriptome of all microbial species in a habitat. Removing ribosomal RNA (rRNA) reads in metatranscriptomic data is essential for the study of microbial gene expression. Although several methods are developed, all of them rely on rRNA databases that contain a limited number of known rRNA sequences and cannot work well on rRNA reads from unknown rRNA sequences. To address this problem, we have developed a novel approach called rRNAFilter. Our method can accurately and rapidly remove rRNA reads from metatranscriptomes without any prior knowledge of known rRNA sequences. Compared with two existing approaches, rRNAFilter has shown comparable performance when working on reads from known rRNA sequences and much better performance when dealing with reads from unknown rRNA sequences.
[Mh] Termos MeSH primário: Algoritmos
RNA Ribossômico/genética
Análise de Sequência de RNA/métodos
Transcriptoma
[Mh] Termos MeSH secundário: Genoma Microbiano
Metagenoma
Padrões de Referência
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Ribosomal)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160910
[St] Status:MEDLINE
[do] DOI:10.1089/cmb.2016.0113



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