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  1 / 25701 MEDLINE  
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[PMID]:29389966
[Au] Autor:Reyes-Velasco J; Manthey JD; Bourgeois Y; Freilich X; Boissinot S
[Ad] Endereço:New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
[Ti] Título:Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data.
[So] Source:PLoS One;13(2):e0190440, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.
[Mh] Termos MeSH primário: Anuros/classificação
Genoma
Filogeografia
Polimorfismo de Nucleotídeo Único
[Mh] Termos MeSH secundário: Animais
Anuros/genética
Código de Barras de DNA Taxonômico
DNA Mitocondrial/genética
Ecossistema
Etiópia
Evolução Molecular
Reação em Cadeia da Polimerase
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[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:180202
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190440


  2 / 25701 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


  3 / 25701 MEDLINE  
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[PMID]:29220445
[Au] Autor:Chen Y; Shi M; Zhang W; Cheng Y; Wang Y; Xia XQ
[Ad] Endereço:Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
[Ti] Título:The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: http://bioinfo.ihb.ac.cn/gcgd.
[Mh] Termos MeSH primário: Carpas/genética
Bases de Dados Genéticas
Genoma/genética
Anotação de Sequência Molecular/métodos
[Mh] Termos MeSH secundário: Animais
Repetições de Microssatélites/genética
Alinhamento de Sequência
Transcriptoma/genética
[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/bax051


  4 / 25701 MEDLINE  
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[PMID]:29220443
[Au] Autor:Rosikiewicz W; Kabza M; Kosinski JG; Ciomborowska-Basheer J; Kubiak MR; Makalowska I
[Ad] Endereço:Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.
[Ti] Título:RetrogeneDB-a database of plant and animal retrocopies.
[So] Source:Database (Oxford);2017, 2017 Jan 01.
[Is] ISSN:1758-0463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Database URL: http://yeti.amu.edu.pl/retrogenedb. Secondary database URL: http://rhesus.amu.edu.pl/retrogenedb.
[Mh] Termos MeSH primário: Bases de Dados Genéticas
Eucariotos/genética
Genoma/genética
Plantas/genética
RNA/genética
Análise de Sequência de RNA
[Mh] Termos MeSH secundário: Animais
Etiquetas de Sequências Expressas
Filogenia
Interface Usuário-Computador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA)
[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/bax038


  5 / 25701 MEDLINE  
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[PMID]:29212445
[Au] Autor:Lyubetsky V; Gershgorin R; Gorbunov K
[Ad] Endereço:Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia.
[Ti] Título:Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming.
[So] Source:BMC Bioinformatics;18(1):537, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding a gene. Gene lengths, nucleotide composition, and intergenic regions are ignored. Although highly incomplete, such structure can be used in many cases, e.g., to reconstruct phylogeny and evolutionary events, to identify gene synteny, regulatory elements and promoters (considering highly conserved elements), etc. Three problems are considered; all assume unequal gene content and the presence of gene paralogs. The distance problem is to determine the minimum number of operations required to transform one chromosome structure into another and the corresponding transformation itself including the identification of paralogs in two structures. We use the DCJ model which is one of the most studied combinatorial rearrangement models. Double-, sesqui-, and single-operations as well as deletion and insertion of a chromosome region are considered in the model; the single ones comprise cut and join. In the reconstruction problem, a phylogenetic tree with chromosome structures in the leaves is given. It is necessary to assign the structures to inner nodes of the tree to minimize the sum of distances between terminal structures of each edge and to identify the mutual paralogs in a fairly large set of structures. A linear algorithm is known for the distance problem without paralogs, while the presence of paralogs makes it NP-hard. If paralogs are allowed but the insertion and deletion operations are missing (and special constraints are imposed), the reduction of the distance problem to integer linear programming is known. Apparently, the reconstruction problem is NP-hard even in the absence of paralogs. The problem of contigs is to find the optimal arrangements for each given set of contigs, which also includes the mutual identification of paralogs. RESULTS: We proved that these problems can be reduced to integer linear programming formulations, which allows an algorithm to redefine the problems to implement a very special case of the integer linear programming tool. The results were tested on synthetic and biological samples. CONCLUSIONS: Three well-known problems were reduced to a very special case of integer linear programming, which is a new method of their solutions. Integer linear programming is clearly among the main computational methods and, as generally accepted, is fast on average; in particular, computation systems specifically targeted at it are available. The challenges are to reduce the size of the corresponding integer linear programming formulations and to incorporate a more detailed biological concept in our model of the reconstruction.
[Mh] Termos MeSH primário: Estruturas Cromossômicas
Genoma
Modelos Genéticos
Programação Linear
[Mh] Termos MeSH secundário: Evolução Biológica
Biologia Computacional
Filogenia
[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:171208
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1944-x


  6 / 25701 MEDLINE  
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[PMID]:28453853
[Au] Autor:Seppälä H; Virtanen E; Saarela M; Laine P; Paulín L; Mannonen L; Auvinen P; Auvinen E
[Ad] Endereço:Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
[Ti] Título:Single-Molecule Sequencing Revealing the Presence of Distinct JC Polyomavirus Populations in Patients With Progressive Multifocal Leukoencephalopathy.
[So] Source:J Infect Dis;215(6):889-895, 2017 03 15.
[Is] ISSN:1537-6613
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Background: Progressive multifocal leukoencephalopathy (PML) is a fatal disease caused by reactivation of JC polyomavirus (JCPyV) in immunosuppressed individuals and lytic infection by neurotropic JCPyV in glial cells. The exact content of neurotropic mutations within individual JCPyV strains has not been studied to our knowledge. Methods: We exploited the capacity of single-molecule real-time sequencing technology to determine the sequence of complete JCPyV genomes in single reads. The method was used to precisely characterize individual neurotropic JCPyV strains of 3 patients with PML without the bias caused by assembly of short sequence reads. Results: In the cerebrospinal fluid sample of a 73-year-old woman with rapid PML onset, 3 distinct JCPyV populations could be identified. All viral populations were characterized by rearrangements within the noncoding regulatory region (NCCR) and 1 point mutation, S267L in the VP1 gene, suggestive of neurotropic strains. One patient with PML had a single neurotropic strain with rearranged NCCR, and 1 patient had a single strain with small NCCR alterations. Conclusions: We report here, for the first time, full characterization of individual neurotropic JCPyV strains in the cerebrospinal fluid of patients with PML. It remains to be established whether PML pathogenesis is driven by one or several neurotropic strains in an individual.
[Mh] Termos MeSH primário: Proteínas do Capsídeo/genética
Líquido Cefalorraquidiano/virologia
Vírus JC/isolamento & purificação
Leucoencefalopatia Multifocal Progressiva/virologia
[Mh] Termos MeSH secundário: Idoso
Idoso de 80 Anos ou mais
Feminino
Finlândia
Genoma
Seres Humanos
Vírus JC/genética
Masculino
Meia-Idade
Mutação
Reação em Cadeia da Polimerase
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Capsid Proteins); 0 (VP1 protein, polyomavirus)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/infdis/jiw399


  7 / 25701 MEDLINE  
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[PMID]:28453670
[Au] Autor:Adams RH; Schield DR; Card DC; Blackmon H; Castoe TA
[Ad] Endereço:Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA.
[Ti] Título:GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data.
[So] Source:Bioinformatics;33(9):1414-1415, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: We introduce GppFst, an open source R package that generates posterior predictive distributions of FST and dx under a neutral coalescent model to identify putative targets of selection from genomic data. Availability and Implementation: GppFst is available at ( https://github.com/radamsRHA/GppFst ). Contact: todd.castoe@uta.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Loci Gênicos
Genética Populacional/métodos
Modelos Genéticos
Polimorfismo de Nucleotídeo Único
Software
[Mh] Termos MeSH secundário: Algoritmos
Animais
Crotalus/genética
Genoma
Genômica/métodos
[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:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw795


  8 / 25701 MEDLINE  
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[PMID]:29237399
[Au] Autor:Ruiz-Arenas C; González JR
[Ad] Endereço:ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.
[Ti] Título:Redundancy analysis allows improved detection of methylation changes in large genomic regions.
[So] Source:BMC Bioinformatics;18(1):553, 2017 Dec 14.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: DNA methylation is an epigenetic process that regulates gene expression. Methylation can be modified by environmental exposures and changes in the methylation patterns have been associated with diseases. Methylation microarrays measure methylation levels at more than 450,000 CpGs in a single experiment, and the most common analysis strategy is to perform a single probe analysis to find methylation probes associated with the outcome of interest. However, methylation changes usually occur at the regional level: for example, genomic structural variants can affect methylation patterns in regions up to several megabases in length. Existing DMR methods provide lists of Differentially Methylated Regions (DMRs) of up to only few kilobases in length, and cannot check if a target region is differentially methylated. Therefore, these methods are not suitable to evaluate methylation changes in large regions. To address these limitations, we developed a new DMR approach based on redundancy analysis (RDA) that assesses whether a target region is differentially methylated. RESULTS: Using simulated and real datasets, we compared our approach to three common DMR detection methods (Bumphunter, blockFinder, and DMRcate). We found that Bumphunter underestimated methylation changes and blockFinder showed poor performance. DMRcate showed poor power in the simulated datasets and low specificity in the real data analysis. Our method showed very high performance in all simulation settings, even with small sample sizes and subtle methylation changes, while controlling type I error. Other advantages of our method are: 1) it estimates the degree of association between the DMR and the outcome; 2) it can analyze a targeted or region of interest; and 3) it can evaluate the simultaneous effects of different variables. The proposed methodology is implemented in MEAL, a Bioconductor package designed to facilitate the analysis of methylation data. CONCLUSIONS: We propose a multivariate approach to decipher whether an outcome of interest alters the methylation pattern of a region of interest. The method is designed to analyze large target genomic regions and outperforms the three most popular methods for detecting DMRs. Our method can evaluate factors with more than two levels or the simultaneous effect of more than one continuous variable, which is not possible with the state-of-the-art methods.
[Mh] Termos MeSH primário: Metilação de DNA/genética
Genoma/genética
Genômica/métodos
[Mh] Termos MeSH secundário: Neoplasias da Mama/genética
Bases de Dados Genéticas
Epigênese Genética
Feminino
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171215
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1986-0


  9 / 25701 MEDLINE  
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[PMID]:29191179
[Au] Autor:Fierst JL; Murdock DA
[Ad] Endereço:Department of Biological Sciences, University of Alabama, Tuscaloosa, 35487, AL, USA. jlfierst@ua.edu.
[Ti] Título:Decontaminating eukaryotic genome assemblies with machine learning.
[So] Source:BMC Bioinformatics;18(1):533, 2017 Dec 01.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few existing methods for rigorously decontaminating eukaryotic assemblies. Those that do exist filter sequences based on nucleotide similarity to contaminants and risk eliminating sequences from the target organism. RESULTS: We introduce a novel application of an established machine learning method, a decision tree, that can rigorously classify sequences. The major strength of the decision tree is that it can take any measured feature as input and does not require a priori identification of significant descriptors. We use the decision tree to classify de novo assembled sequences and compare the method to published protocols. CONCLUSIONS: A decision tree performs better than existing methods when classifying sequences in eukaryotic de novo assemblies. It is efficient, readily implemented, and accurately identifies target and contaminant sequences. Importantly, a decision tree can be used to classify sequences according to measured descriptors and has potentially many uses in distilling biological datasets.
[Mh] Termos MeSH primário: Caenorhabditis/genética
Aprendizado de Máquina
[Mh] Termos MeSH secundário: Animais
Composição de Bases
DNA de Helmintos/química
DNA de Helmintos/isolamento & purificação
DNA de Helmintos/metabolismo
Bases de Dados Genéticas
Genoma
Sequenciamento de Nucleotídeos em Larga Escala
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Helminth)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171202
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1941-0


  10 / 25701 MEDLINE  
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[PMID]:29179672
[Au] Autor:Huang YT; Huang YW
[Ad] Endereço:Department of Computer Science and Information Engineering, National Chuang Cheng University, Chiayi, Taiwan. ythuang@cs.ccu.edu.tw.
[Ti] Título:An efficient error correction algorithm using FM-index.
[So] Source:BMC Bioinformatics;18(1):524, 2017 Nov 28.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent de novo assembly, error correction is necessary prior to assembly. However, existing correction methods still face trade-offs among correction power, accuracy, and speed. RESULTS: We develop a novel overlap-based error correction algorithm using FM-index (called FMOE). FMOE first identifies overlapping reads by aligning a query read simultaneously against multiple reads compressed by FM-index. Subsequently, sequencing errors are corrected by k-mer voting from overlapping reads only. The experimental results indicate that FMOE has highest correction power with comparable accuracy and speed. Our algorithm performs better in long-read than short-read datasets when compared with others. The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads. CONCLUSIONS: FMOE is freely available at https://github.com/ythuang0522/FMOC .
[Mh] Termos MeSH primário: Algoritmos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
[Mh] Termos MeSH secundário: Animais
Bactérias/genética
Sequência de Bases
Caenorhabditis elegans/genética
Genoma
Alinhamento de Sequência
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1940-1



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