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[PMID]:29202689
[Au] Autor:Jalili V; Matteucci M; Masseroli M; Ceri S
[Ad] Endereço:Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, 20133, Italy. vahid.jalili@polimi.it.
[Ti] Título:Explorative visual analytics on interval-based genomic data and their metadata.
[So] Source:BMC Bioinformatics;18(1):536, 2017 Dec 04.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: With the wide-spreading of public repositories of NGS processed data, the availability of user-friendly and effective tools for data exploration, analysis and visualization is becoming very relevant. These tools enable interactive analytics, an exploratory approach for the seamless "sense-making" of data through on-the-fly integration of analysis and visualization phases, suggested not only for evaluating processing results, but also for designing and adapting NGS data analysis pipelines. RESULTS: This paper presents abstractions for supporting the early analysis of NGS processed data and their implementation in an associated tool, named GenoMetric Space Explorer (GeMSE). This tool serves the needs of the GenoMetric Query Language, an innovative cloud-based system for computing complex queries over heterogeneous processed data. It can also be used starting from any text files in standard BED, BroadPeak, NarrowPeak, GTF, or general tab-delimited format, containing numerical features of genomic regions; metadata can be provided as text files in tab-delimited attribute-value format. GeMSE allows interactive analytics, consisting of on-the-fly cycling among steps of data exploration, analysis and visualization that help biologists and bioinformaticians in making sense of heterogeneous genomic datasets. By means of an explorative interaction support, users can trace past activities and quickly recover their results, seamlessly going backward and forward in the analysis steps and comparative visualizations of heatmaps. CONCLUSIONS: GeMSE effective application and practical usefulness is demonstrated through significant use cases of biological interest. GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/ , and its source code is available at https://github.com/Genometric/GeMSE under GPLv3 open-source license.
[Mh] Termos MeSH primário: Bases de Dados Genéticas
Genômica/métodos
Metadados
[Mh] Termos MeSH secundário: Células A549
Dexametasona/farmacologia
Etanol/farmacologia
Seres Humanos
Modelos Teóricos
Reconhecimento Automatizado de Padrão
Mapeamento de Interação de Proteínas
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
3K9958V90M (Ethanol); 7S5I7G3JQL (Dexamethasone)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1945-9


  2 / 34753 MEDLINE  
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[PMID]:29179671
[Au] Autor:Hudaiberdiev S; Shmakov S; Wolf YI; Terns MP; Makarova KS; Koonin EV
[Ad] Endereço:National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
[Ti] Título:Phylogenomics of Cas4 family nucleases.
[So] Source:BMC Evol Biol;17(1):232, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles. CONCLUSIONS: Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.
[Mh] Termos MeSH primário: Sistemas CRISPR-Cas/genética
Endonucleases/genética
Genômica
Família Multigênica
[Mh] Termos MeSH secundário: Archaea/enzimologia
Archaea/genética
Bactérias/enzimologia
Bactérias/genética
Sequência de Bases
Elementos de DNA Transponíveis/genética
Transferência Genética Horizontal/genética
Loci Gênicos
Genoma Arqueal
Genoma Bacteriano
Filogenia
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1081-1


  3 / 34753 MEDLINE  
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[PMID]:29458535
[Au] Autor:Shahin K; Bouzari M; Wang R
[Ad] Endereço:1​Department of Biology, Faculty of Sciences, University of Isfahan, Hezar Jereeb Street, 81746-73441, Isfahan, Iran.
[Ti] Título:Isolation, characterization and genomic analysis of a novel lytic bacteriophage vB_SsoS-ISF002 infecting Shigella sonnei and Shigella flexneri.
[So] Source:J Med Microbiol;67(3):376-386, 2018 Mar.
[Is] ISSN:1473-5644
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:PURPOSE: Shigellosis is one of the most important food-borne and water-borne diseases worldwide. Although antibiotics are considered as efficient agents for shigellosis treatment, improper use of these has led to the emergence of antibiotic-resistant Shigella spp. Therefore, finding a new strategy as alternative treatment seems necessary. METHODOLOGY: Different samples from a wastewater treatment plant were used to isolate Shigella spp. specific phages. Physiological properties were determined, and genomic analysis was also carried out. RESULTS: A virulent Siphoviridae bacteriophage, vB_SsoS-ISF002, was isolated from urban wastewater in Iran and showed infectivity to different isolates of both Shigella sonnei and Shigella flexneri. vB_SsoS-ISF002 was stable at different pH values and temperatures. It had a short latent period (15 min), a large burst size (76±9 p.f.u. cell ) and appropriate lytic activity especially at high MOI. Its genome (dsDNA) was 50 564 bp with 45.53 % GC content and 76 predicted open reading frames. According to comparative genomic analysis and phylogenic tree construction, vB_SsoS-ISF002 was considered as a member of the T1virus genus. CONCLUSION: These results indicated that vB_SsoS-ISF002 is a novel virulent T1virus phage and may have potential as an alternative treatment for shigellosis.
[Mh] Termos MeSH primário: Genoma Viral
Shigella flexneri/virologia
Shigella sonnei/virologia
Siphoviridae/genética
Siphoviridae/isolamento & purificação
[Mh] Termos MeSH secundário: Antibacterianos/farmacologia
Composição de Bases
DNA Viral
Disenteria Bacilar/terapia
Genômica
Seres Humanos
Terapia por Fagos
Filogenia
Análise de Sequência de DNA
Shigella flexneri/efeitos dos fármacos
Shigella sonnei/efeitos dos fármacos
Siphoviridae/classificação
Siphoviridae/fisiologia
Águas Residuais/microbiologia
Águas Residuais/virologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (DNA, Viral); 0 (Waste Water)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180221
[St] Status:MEDLINE
[do] DOI:10.1099/jmm.0.000683


  4 / 34753 MEDLINE  
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[PMID]:29191895
[Au] Autor:Eisenberg R; Varmus H
[Ad] Endereço:University of Michigan Law School, Ann Arbor, MI 48109, USA. rse@umich.edu varmus@med.cornell.edu.
[Ti] Título:Insurance for broad genomic tests in oncology.
[So] Source:Science;358(6367):1133-1134, 2017 12 01.
[Is] ISSN:1095-9203
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Análise Mutacional de DNA/economia
Testes Genéticos/economia
Seguro
Neoplasias/genética
[Mh] Termos MeSH secundário: Análise Custo-Benefício
Genes erbB-1
Genômica/economia
Seres Humanos
Oncologia/economia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171202
[St] Status:MEDLINE
[do] DOI:10.1126/science.aao6708


  5 / 34753 MEDLINE  
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[PMID]:29244014
[Au] Autor:Aganezov SS; Alekseyev MA
[Ad] Endereço:Princeton University, 35 Olden St., Princeton, 08450, NJ, USA. aganezov@cs.princeton.edu.
[Ti] Título:CAMSA: a tool for comparative analysis and merging of scaffold assemblies.
[So] Source:BMC Bioinformatics;18(Suppl 15):496, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually. RESULTS: We present CAMSA-a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time. CONCLUSIONS: CAMSA addresses the current deficiency of tools for automated comparison and analysis of multiple assemblies of the same set scaffolds. Since there exist numerous methods and techniques for scaffold assembly, identifying similarities and dissimilarities across assemblies produced by different methods is beneficial both for the developers of scaffold assembly algorithms and for the researchers focused on improving draft assemblies of specific organisms.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Genômica/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Genoma
Alinhamento de Sequência
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1919-y


  6 / 34753 MEDLINE  
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[PMID]:29220446
[Au] Autor:Chen M; Henry N; Almsaeed A; Zhou X; Wegrzyn J; Ficklin S; Staton M
[Ad] Endereço:Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
[Ti] Título:New extension software modules to enhance searching and display of transcriptome data in Tripal databases.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch. Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression.
[Mh] Termos MeSH primário: Bases de Dados Genéticas
Perfilação da Expressão Gênica/métodos
Genômica/métodos
Software
Transcriptoma/genética
[Mh] Termos MeSH secundário: Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax052


  7 / 34753 MEDLINE  
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[PMID]:29220442
[Au] Autor:Wiewiórka MS; Wysakowicz DP; Okoniewski MJ; Gambin T
[Ad] Endereço:Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, Warsaw 00-665, Poland.
[Ti] Título:Benchmarking distributed data warehouse solutions for storing genomic variant information.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: https://github.com/ZSI-Bio/variantsdwh.
[Mh] Termos MeSH primário: Armazenamento de Dados
Sistemas de Gerenciamento de Base de Dados
Bases de Dados Genéticas
Genômica/métodos
[Mh] Termos MeSH secundário: Benchmarking
Seres Humanos
Medicina de Precisão
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax049


  8 / 34753 MEDLINE  
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[PMID]:29220437
[Au] Autor:Torres F; Arias-Carrasco R; Caris-Maldonado JC; Barral A; Maracaja-Coutinho V; De Queiroz ATL
[Ad] Endereço:Centro de Pesquisas Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil.
[Ti] Título:LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: www.leishdb.com.
[Mh] Termos MeSH primário: Genes de Protozoários/genética
Leishmania braziliensis/genética
RNA não Traduzido/genética
Interface Usuário-Computador
[Mh] Termos MeSH secundário: Genômica
Internet
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Untranslated)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1093/database/bax047


  9 / 34753 MEDLINE  
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[PMID]:29212440
[Au] Autor:Gdanetz K; Benucci GMN; Vande Pol N; Bonito G
[Ad] Endereço:Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA.
[Ti] Título:CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences.
[So] Source:BMC Bioinformatics;18(1):538, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. RESULTS: Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. CONCLUSIONS: Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX.
[Mh] Termos MeSH primário: DNA Fúngico/genética
DNA Intergênico/genética
Fungos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Software
[Mh] Termos MeSH secundário: Microbiologia Ambiental
Fungos/classificação
Fungos/genética
Genoma Fúngico/genética
Genômica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Fungal); 0 (DNA, Intergenic)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1952-x


  10 / 34753 MEDLINE  
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[PMID]:28453680
[Au] Autor:Holtz Y; David JL; Ranwez V
[Ad] Endereço:Montpellier Supagro, Department BE, UMR AGAP, 34060 Montpellier, France.
[Ti] Título:The genetic map comparator: a user-friendly application to display and compare genetic maps.
[So] Source:Bioinformatics;33(9):1387-1388, 2017 05 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Motivation: Marker-assisted selection strongly relies on genetic maps to accelerate breeding programs. High-density maps are now available for numerous species. Dedicated tools are required to compare several high-density maps on the basis of their key characteristics, while pinpointing their differences and similarities. Results: We developed the Genetic Map Comparator-a web-based application for easy comparison of different maps according to their key statistics and the relative positions of common markers. Availability and Implementation: The Genetic Map Comparator is available online at: http://bioweb.supagro.inra.fr/geneticMapComparator. The source code is freely available on GitHub under the under the CeCILL general public license: https://github.com/holtzy/GenMap-Comparator. Contact: Holtz@supagro.fr; Ranwez@supagro.fr.
[Mh] Termos MeSH primário: Genômica/métodos
Análise de Sequência de DNA/métodos
Software
[Mh] Termos MeSH secundário: Resistência à Doença/genética
Genes de Plantas
Doenças das Plantas/genética
Locos de Características Quantitativas
Triticum/genética
Triticum/virologia
Viroses/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw816



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