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Whole genome alignment

Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Md Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill-Sup Nou
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA...
2018: PloS One
Yan Liu, Xiaoyu Guan, Shengnan Liu, Meng Yang, Junhui Ren, Meng Guo, Zhihui Huang, Yaowei Zhang
Chinese cabbage ( Brassica rapa L. ssp . pekinensis ) is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor) family proteins are plant-specific transcription factors (TFs) and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa , TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b ...
March 14, 2018: International Journal of Molecular Sciences
Brittney N Keel, Warren M Snelling
Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Efficient alignment of the reads onto the reference genome with high accuracy is very important because it determines the global quality of downstream analyses. In this study, we evaluate the performance of three Burrows-Wheeler transform-based mappers, BWA, Bowtie2, and HISAT2, in the context of paired-end Illumina whole-genome sequencing of livestock, using simulated sequence data sets with varying sequence read lengths, insert sizes, and levels of genomic coverage, as well as five real data sets...
2018: Frontiers in Genetics
Jonathan Vadnal, Olivia G Granger, Ramesh Ratnappan, Ioannis Eleftherianos, Damien M O'Halloran, John M Hawdon
Interest has recently grown in developing the entomopathogenic nematode Heterorhabditis bacteriophora as a model to genetically dissect the process of parasitic infection. Despite the availability of a full genome assembly, there is substantial variation in gene model accuracy. Here, a methodology is presented for leveraging RNA-seq evidence to generate improved annotations using ab initio gene prediction software. After alignment of reads and subsequent generation of a RNA-seq supported annotation, the new gene prediction models were verified on a selection of genes by comparison with sequenced 5' and 3' rapid amplification of cDNA ends (RACE) products...
March 9, 2018: International Journal for Parasitology
Laura Becker, Stephan Fuchs, Yvonne Pfeifer, Torsten Semmler, Tim Eckmanns, Gerit Korr, Dagmar Sissolak, Michael Friedrichs, Edith Zill, Mei-Lin Tung, Christian Dohle, Martin Kaase, Sören Gatermann, Holger Rüssmann, Matthias Steglich, Sebastian Haller, Guido Werner
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K...
2018: Frontiers in Microbiology
Tim Stuart, Sam Buckberry, Ryan Lister
DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for analysis of DNA methylation. Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required...
2018: Methods in Molecular Biology
Lamia Yacoubi, Ségolène Brichler, Frédéric Le Gal, Henda Triki, Emmanuel Gordien
While Tunisia is endemic for hepatitis B virus (HBV), a recent large-scale retrospective study, revealed a very low prevalence (2%) of hepatitis Delta virus (HDV) (Yacoubi et al. in J Clin Virol 72:126-132, 2015). All strains were classified within the genotype 1 (HDV-1) as assessed by nucleotide sequencing of the so-called 'R0' region of the genome described previously. In this study, we aimed to determine the full-length genome sequence of HDV isolates in order to fully characterize the HDV strains spreading in Tunisia...
March 7, 2018: Archives of Virology
Xiaoyu Yu, Oleg N Reva
Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities...
2018: Evolutionary Bioinformatics Online
Toolika Singh, Michaela Fakiola, Joyce Oommen, Akhil Pratap Singh, Abhishek K Singh, Noel Smith, Jaya Chakravarty, Shyam Sundar, Jenefer M Blackwell
HLA-DRB1 is the major genetic risk factor for visceral leishmaniasis (VL). We used SNP2HLA to impute HLA-DRB1 alleles and SNPTEST to carry out association analyses in 889 human cases and 977 controls from India. NetMHCIIpan 2.1 was used to map epitopes and binding affinities across 49 Leishmania vaccine candidates, as well as across peptide epitopes captured from dendritic cells treated with crude Leishmania Ag and identified using mass spectrometry and alignment to amino acid sequences of a reference Leishmania genome...
March 5, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Fedor M Naumenko, Irina I Abnizova, Nathan Beka, Mikhail A Genaev, Yuriy L Orlov
BACKGROUND: The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome. RESULTS: We investigated whether a single chromosome mapping causes any artefacts in the alignments' performances. In this paper, we compared the accuracy of the performance of seven aligners on well-controlled simulated benchmark data which was sampled from a single chromosome and also from a whole genome...
February 9, 2018: BMC Genomics
Unni K Samavedam, Nina Mitschker, Anika Kasprick, Katja Bieber, Enno Schmidt, Tamás Laskay, Andreas Recke, S Goletz, Gestur Vidarsson, Franziska S Schulze, Mikko Armbrust, Katharina Schulze Dieckhoff, Hendri H Pas, Marcel F Jonkman, Kathrin Kalies, Detlef Zillikens, Yask Gupta, Saleh M Ibrahim, Ralf J Ludwig
Because of the morbidity and limited therapeutic options of autoimmune diseases, there is a high, and thus far, unmet medical need for development of novel treatments. Pemphigoid diseases, such as epidermolysis bullosa acquisita (EBA), are prototypical autoimmune diseases that are caused by autoantibodies targeting structural proteins of the skin, leading to inflammation, mediated by myeloid cells. To identify novel treatment targets, we performed cutaneous genome-wide mRNA expression profiling in 190 outbred mice after EBA induction...
2018: Frontiers in Immunology
Theodore S Kalbfleisch, Brenda M Murdoch, Timothy P L Smith, James D Murdoch, Michael P Heaton, Stephanie D McKay
Background : Moose ( Alces alces ) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US).  Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America.  Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data...
2018: F1000Research
Daniel Castillo, Diliana Pérez-Reytor, Nicolás Plaza, Sebastián Ramírez-Araya, Carlos J Blondel, Gino Corsini, Roberto Bastías, David E Loyola, Víctor Jaña, Leonardo Pavez, Katherine García
Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. As reported in other countries, after the rise and fall of the pandemic strain in Chile, other post-pandemic strains have been associated with clinical cases, including strains lacking the major toxins TDH and TRH. Since the presence or absence of tdh and trh genes has been used for diagnostic purposes and as a proxy of the virulence of V. parahaemolyticus isolates, the understanding of virulence in V. parahaemolyticus strains lacking toxins is essential to detect these strains present in water and marine products to avoid possible food-borne infection...
2018: Frontiers in Microbiology
Hülya Kaya, Henrik Hasman, Jesper Larsen, Marc Stegger, Thor Bech Johannesen, Rosa Lundbye Allesøe, Camilla Koldbæk Lemvigh, Frank Møller Aarestrup, Ole Lund, Anders Rhod Larsen
Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCC mec ), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCC mec is less trivial because of its heterogeneity...
January 2018: MSphere
Yuanqiu Dong, Bo Li, Lizhi Zhou
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp...
February 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I Nakaya, Vinicius Maracaja-Coutinho
BACKGROUND: The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills...
February 17, 2018: BMC Bioinformatics
Yung-Hao Ching, Jih-I Yeh, Wen-Lang Fan, Ko-Chen Chen, Man-Chieh Yeh, Peng Yeong Woon, Yuan-Chieh Lee
BACKGROUND/PURPOSE: To identify the underlying genetic cause of a Taiwanese family with autosomal dominant cerulean cataract. METHODS: A three-generation cerulean cataract family with 13 affected and 13 normal was identified. Whole exome sequencing, whole genome single nucleotide polymorphism genotyping and haplotype analysis, and fine mapping using polymorphic short tandem repeat markers were used to identify the causative gene mutation. RESULTS: Whole genome single nucleotide polymorphism genotyping and haplotype analysis mapped the candidate disease loci to chromosome 18 and chromosome 22...
January 27, 2018: Journal of the Formosan Medical Association, Taiwan Yi Zhi
Kairi Raime, Maido Remm
Polymerase chain reaction and different barcoding methods commonly used for plant identification from metagenomics samples are based on the amplification of a limited number of pre-selected barcoding regions. These methods are often inapplicable due to DNA degradation, low amplification success or low species discriminative power of selected genomic regions. Here we introduce a method for the rapid identification of plant taxon-specific k-mers, that is applicable for the fast detection of plant taxa directly from raw sequencing reads without aligning, mapping or assembling the reads...
2018: Frontiers in Plant Science
Adam Peritz, George C Paoli, Chin-Yi Chen, Andrew G Gehring
DNA sequencing and other DNA-based methods are now broadly used for detection and identification of bacterial foodborne pathogens. For the identification of foodborne bacterial pathogens, taxonomic assignments must be made to the species or even subspecies level. Long-read DNA sequencing provides finer taxonomic resolution than short-read sequencing. Here, we demonstrate the potential of long-read shotgun sequencing obtained from the Oxford Nanopore Technologies (ONT) MinION single-molecule sequencer, in combination with the Basic Local Alignment Search Tool (BLAST) with custom sequence databases, for foodborne pathogen identification...
January 27, 2018: Analytical and Bioanalytical Chemistry
Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin
The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. Despite its broad utility, MUMmer3 has limitations that can make it difficult to use for large genomes and for the very large sequence data sets that are common today...
January 26, 2018: PLoS Computational Biology
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