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Whole genome alignment

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https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#1
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29764365/towards-pan-genome-read-alignment-to-improve-variation-calling
#2
Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29761214/analysis-of-resistance-genes-of-clinical-pannonibacter-phragmitetus-strain-31801-by-complete-genome-sequencing
#3
De-Song Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database...
May 14, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29755420/characterization-of-two-novel-bacteriophages-infecting-multidrug-resistant-mdr-acinetobacter-baumannii-and-evaluation-of-their-therapeutic-efficacy-in-vivo
#4
Kyoungeun Cha, Hynu K Oh, Jae Y Jang, Yunyeol Jo, Won K Kim, Geon U Ha, Kwan S Ko, Heejoon Myung
Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of Caudovirales as their morphology observed under an electron microscope. Their genomes were double stranded linear DNAs of 42,312 base pairs and 40,260 base pairs, respectively. The two phages were distinct from known Acinetobacter phages when whole genome sequences were compared...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29746212/harnessing-omics-big-data-in-nine-vertebrate-species-by-genome-wide-prioritization-of-sequence-variants-with-the-highest-predicted-deleterious-effect-on-protein-function
#5
Vita Rozman, Tanja Kunej
Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish...
May 10, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29739321/comparison-of-the-chinese-bamboo-partridge-and-red-junglefowl-genome-sequences-highlights-the-importance-of-demography-in-genome-evolution
#6
G P Tiley, R T Kimball, E L Braun, J G Burleigh
BACKGROUND: Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29728590/phylogenetic-analyses-and-in-seedling-expression-of-ammonium-and-nitrate-transporters-in-wheat
#7
Prabin Bajgain, Blake Russell, Mohsen Mohammadi
Plants deploy several ammonium transporter (AMT) and nitrate transporter (NRT) genes to acquire NH4 + and NO3 - from the soil into the roots and then transport them to other plant organs. Coding sequences of wheat genes obtained from ENSEMBL were aligned to known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous genes. Bayesian phylogenetic relationships among these genes showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2)...
May 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29724166/surveying-alignment-free-features-for-ortholog-detection-in-related-yeast-proteomes-by-using-supervised-big-data-classifiers
#8
Deborah Galpert, Alberto Fernández, Francisco Herrera, Agostinho Antunes, Reinaldo Molina-Ruiz, Guillermin Agüero-Chapin
BACKGROUND: The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011)...
May 3, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29717164/comparative-analyses-of-whole-genome-protein-sequences-from-multiple-organisms
#9
Makio Yokono, Soichirou Satoh, Ayumi Tanaka
Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29703150/omgene-mutual-improvement-of-gene-models-through-optimisation-of-evolutionary-conservation
#10
Michael P Dunne, Steven Kelly
BACKGROUND: The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequently disagree on the model for a given predicted gene, with some or all of the variant gene models often failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29697369/eagle-explicit-alternative-genome-likelihood-evaluator
#11
Tony Kuo, Martin C Frith, Jun Sese, Paul Horton
BACKGROUND: Reliable detection of genome variations, especially insertions and deletions (indels), from single sample DNA sequencing data remains challenging, partially due to the inherent uncertainty involved in aligning sequencing reads to the reference genome. In practice a variety of ad hoc quality filtering methods are employed to produce more reliable lists of putative variants, but the resulting lists typically still include numerous false positives. Thus it would be desirable to be able to rigorously evaluate the degree to which each putative variant is supported by the data...
April 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29696033/redidb-3-0-a-comprehensive-collection-of-rna-editing-events-in-plant-organellar-genomes
#12
Claudio Lo Giudice, Graziano Pesole, Ernesto Picardi
RNA editing is an important epigenetic mechanism by which genome-encoded transcripts are modified by substitutions, insertions and/or deletions. It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms. In plants, RNA editing occurs mostly by cytidine (C) to uridine (U) conversion in translated regions of organelle mRNAs and tends to modify affected codons restoring evolutionary conserved aminoacid residues. RNA editing has also been described in non-protein coding regions such as group II introns and structural RNAs...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29695831/deletion-at-the-5-end-of-estonian-asfv-strains-associated-with-an-attenuated-phenotype
#13
Laura Zani, Jan Hendrik Forth, Leonie Forth, Imbi Nurmoja, Simone Leidenberger, Julia Henke, Jolene Carlson, Christiane Breidenstein, Arvo Viltrop, Dirk Höper, Carola Sauter-Louis, Martin Beer, Sandra Blome
African swine fever (ASF) was introduced into the Eastern European Union in 2014 and led to considerable mortality among wild boar. In contrast, unexpected high antibody prevalence was reported in hunted wild boar in north-eastern Estonia. One of the causative virus strains was recently characterized. While it still showed rather high virulence in the majority of experimentally infected animals, one animal survived and recovered completely. Here, we report on the follow-up characterization of the isolate obtained from the survivor in the acute phase of infection...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29673790/molecular-detection-and-quantification-of-viable-probiotic-strains-in-animal-feedstuffs-using-the-commercial-direct-fed-microbial-lactobacillus-animalis-np51-as-a-model
#14
D I Ayala, J Chen, M Bugarel, G H Loneragan, H C den Bakker, K R Kottapalli, M M Brashears, K K Nightingale
Lactobacillus animalis NP51 is a direct-fed microbial strain (DFM) extensively used as a pre-harvest food safety mitigation in feedlot cattle due to its antagonistic effects against human foodborne pathogens such as Salmonella and Escherichia coli O157:H7. NP51 not only promotes overall gut health but interferes with the ability of these pathogens to colonize the gastrointestinal tract of cattle. As a result, NP51 reduces fecal shedding of Salmonella and E. coli O157:H7 in cattle presented for harvest and the load of these pathogens that enter the human food chain...
April 16, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29664468/unifying-cancer-and-normal-rna-sequencing-data-from-different-sources
#15
Qingguo Wang, Joshua Armenia, Chao Zhang, Alexander V Penson, Ed Reznik, Liguo Zhang, Thais Minet, Angelica Ochoa, Benjamin E Gross, Christine A Iacobuzio-Donahue, Doron Betel, Barry S Taylor, Jianjiong Gao, Nikolaus Schultz
Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing...
April 17, 2018: Scientific Data
https://www.readbyqxmd.com/read/29662481/-listeria-monocytogenes-sequence-types-121-and-14-repeatedly-isolated-within-one-year-of-sampling-in-a-rabbit-meat-processing-plant-persistence-and-ecophysiology
#16
Frédérique Pasquali, Federica Palma, Laurent Guillier, Alex Lucchi, Alessandra De Cesare, Gerardo Manfreda
Listeria monocytogenes is a foodborne pathogen adapted to survive and persist in multiple environments. Following two previous studies on prevalence and virulence of L. monocytogenes ST121 and ST14 repeatedly collected in a the same rabbit-meat processing plant, the research questions of the present study were to: (1) assess persistence of L. monocytogenes isolates from the rabbit-plant; (2) select genes associated to physiological adaptation to the food-processing environment; (3) compare presence/absence/truncation of these genes in newly sequenced and publicly available ST121 and ST14 genomes...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29659490/a-comparative-genomic-survey-provides-novel-insights-into-molecular-evolution-of-l-aromatic-amino-acid-decarboxylase-in-vertebrates
#17
Yanping Li, Yunyun Lv, Chao Bian, Xinxin You, Li Deng, Qiong Shi
Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad -like gene, which formed a novel AAAD family...
April 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29644997/highly-scalable-generation-of-dna-methylation-profiles-in-single-cells
#18
Ryan M Mulqueen, Dmitry Pokholok, Steven J Norberg, Kristof A Torkenczy, Andrew J Fields, Duanchen Sun, John R Sinnamon, Jay Shendure, Cole Trapnell, Brian J O'Roak, Zheng Xia, Frank J Steemers, Andrew C Adey
We present a highly scalable assay for whole-genome methylation profiling of single cells. We use our approach, single-cell combinatorial indexing for methylation analysis (sci-MET), to produce 3,282 single-cell bisulfite sequencing libraries and achieve read alignment rates of 68 ± 8%. We apply sci-MET to discriminate the cellular identity of a mixture of three human cell lines and to identify excitatory and inhibitory neuronal populations from mouse cortical tissue.
April 9, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29618486/optical-mapping-reveals-a-higher-level-of-genomic-architecture-of-chained-fusions-in-cancer
#19
Eva K F Chan, Daniel L Cameron, Desiree C Petersen, Ruth J Lyons, Benedetta F Baldi, Anthony T Papenfuss, David M Thomas, Vanessa M Hayes
Genomic rearrangements are common in cancer, with demonstrated links to disease progression and treatment response. These rearrangements can be complex, resulting in fusions of multiple chromosomal fragments and generation of derivative chromosomes. While methods exist for detecting individual fusions, they are generally unable to reconstruct complex chained events. To overcome these limitations, we adopted a new optical mapping approach, allowing megabase length genome maps to be reconstructed and rearranged genomes to be visualized without loss of integrity...
April 4, 2018: Genome Research
https://www.readbyqxmd.com/read/29618053/g-anchor-a-novel-approach-for-whole-genome-comparative-mapping-utilising-evolutionary-conserved-dna-sequences
#20
Vasileios Panagiotis E Lenis, Martin Swain, Denis M Larkin
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses...
April 3, 2018: GigaScience
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