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https://www.readbyqxmd.com/read/28334120/svpv-a-structural-variant-prediction-viewer-for-paired-end-sequencing-datasets
#1
Jacob E Munro, Sally L Dunwoodie, Eleni Giannoulatou
Motivation: A wide range of algorithms exist for the prediction of structural variants (SVs) from paired-end whole genome sequencing (WGS) alignments. It is essential for the purpose of quality control to be able to visualize, compare and contrast the data underlying the predictions across multiple different algorithms. Results: We provide the structural variant prediction viewer, a tool which presents a visual summary of the most relevant features for SV prediction from WGS data...
February 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333980/evaluating-alignment-and-variant-calling-software-for-mutation-identification-in-c-elegans-by-whole-genome-sequencing
#2
Harold E Smith, Sijung Yun
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria...
2017: PloS One
https://www.readbyqxmd.com/read/28326674/whole-exome-sequencing-with-genomic-triangulation-implicates-cdh2-encoded-n-cadherin-as-a-novel-pathogenic-substrate-for-arrhythmogenic-cardiomyopathy
#3
Kari L Turkowski, David J Tester, J Martijn Bos, Kristina H Haugaa, Michael J Ackerman
BACKGROUND: Arrhythmogenic cardiomyopathy (ACM) is a heritable disease characterized by fibrofatty replacement of cardiomyocytes, has a prevalence of approximately 1 in 5000 individuals, and accounts for approximately 20% of sudden cardiac death in the young (≤35 years). ACM is most often inherited as an autosomal dominant trait with incomplete penetrance and variable expression. While mutations in several genes that encode key desmosomal proteins underlie about half of all ACM, the remainder is elusive genetically...
March 21, 2017: Congenital Heart Disease
https://www.readbyqxmd.com/read/28323836/single-nucleotide-variants-and-indels-identified-from-whole-genome-re-sequencing-of-guzerat-gyr-girolando-and-holstein-cattle-breeds
#4
Nedenia Bonvino Stafuzza, Adhemar Zerlotini, Francisco Pereira Lobo, Michel Eduardo Beleza Yamagishi, Tatiane Cristina Seleguim Chud, Alexandre Rodrigues Caetano, Danísio Prado Munari, Dorian J Garrick, Marco Antonio Machado, Marta Fonseca Martins, Maria Raquel Carvalho, John Bruce Cole, Marcos Vinicius Gualberto Barbosa da Silva
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel...
2017: PloS One
https://www.readbyqxmd.com/read/28320310/treetoreads-a-pipeline-for-simulating-raw-reads-from-phylogenies
#5
Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E Timme
BACKGROUND: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28279756/analysis-of-ccr5-gene-polymorphisms-in-321-healthy-saudis-using-next-generation-sequencing
#6
Mohammed A Al Balwi, Ali I Hadadi, Wardah Alharbi, Mariam Ballow, Abdulrahman AlAsiri, Abdulkareem AlAbdulrahman, Udayaraja G K, Mohammed Aldrees, Ibrahim AlAbdulkareem, Ali H Hajeer
AIMS: To investigate the extent of CCR5 polymorphism in the healthy Saudi population. METHOD: A total of 321 healthy Saudi individuals were sequenced using the ion Ampliseq™ Exome kit (Life Technologies, USA) on genomic DNA following manufacturer's protocol. Whole Exome Sequencing (WES) reads were aligned to the human reference genome (hg19 build) with Torrent Suite Software (v5.0.2) and the variants were called using the Torrent Variant Caller plugin (v5.0) and imported into Ion Reporter Server (v5...
March 7, 2017: Human Immunology
https://www.readbyqxmd.com/read/28258183/the-bacterial-sequential-markov-coalescent
#7
Nicola De Maio, Daniel J Wilson
Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree...
March 3, 2017: Genetics
https://www.readbyqxmd.com/read/28241897/cloning-molecular-characterization-and-spatial-and-developmental-expression-analysis-of-gpr41-and-gpr43-genes-in-new-zealand-rabbits
#8
C Y Fu, L Liu, Q Gao, X Y Sui, F C Li
Short-chain fatty acids (SCFAs) play a regulatory role in various physiological processes in mammals and act as endogenous ligands for the G protein-coupled receptors (GPR) 41 and 43. The role of GPR41 and GPR43 in mediating SCFA signaling in the rabbit remains unclear. The present study was to investigate the sequence of the GPR41 and GPR43 messenger RNA (mRNA) and their expression pattern in different tissues and developmental stages in New Zealand rabbit. Comparison of genomic sequences in GenBank using the Basic Local Alignment Search Tool program suggested that the New Zealand rabbit GPR41 mRNA has high similarities with the human (84%), bovine (84%) and Capra hircus (84%) genes...
February 28, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28235829/a-dense-brown-trout-salmo-trutta-linkage-map-reveals-recent-chromosomal-rearrangements-in-the-salmo-genus-and-the-impact-of-selection-on-linked-neutral-diversity
#9
Maeva Leitwein, Bruno Guinand, Juliette Pouzadoux, Erick Desmarais, Patrick Berrebi, Pierre-Alexandre Gagnaire
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28225804/an-outbreak-of-acute-respiratory-disease-caused-by-a-virus-associated-rna-ii-gene-mutation-strain-of-human-adenovirus-7-in-china-2015
#10
Xiaoxia Yang, Qiongshu Wang, Beibei Liang, Fuli Wu, Hao Li, Hongbo Liu, Chunyu Sheng, Qiuxia Ma, Chaojie Yang, Jing Xie, Peng Li, Leili Jia, Ligui Wang, Xinying Du, Shaofu Qiu, Hongbin Song
Human adenovirus 7 (HAdV-7) strains are a major cause of acute respiratory disease (ARD) among adults and children, associated with fatal pneumonia. An ARD outbreak caused by HAdV-7 that involved 739 college students was reported in this article. To better understand the underlying cause of this large-scale epidemic, virus strains were isolated from infected patients and sequence variations of the whole genome sequence were detected. Evolutionary trees and alignment results indicated that the major capsid protein genes hexon and fibre were strongly conserved among serotype 7 strains in China at that time...
2017: PloS One
https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#11
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28196958/transcription-profiling-of-bacillus-subtilis-cells-infected-with-ar9-a-giant-phage-encoding-two-multisubunit-rna-polymerases
#12
Daria Lavysh, Maria Sokolova, Marina Slashcheva, Konrad U Förstner, Konstantin Severinov
Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5' ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28168408/ssr-enriched-genetic-linkage-maps-of-bermudagrass-cynodon-dactylon%C3%A2-%C3%A3-%C3%A2-transvaalensis-and-their-comparison-with-allied-plant-genomes
#13
Sameer Khanal, Changsoo Kim, Susan A Auckland, Lisa K Rainville, Jeevan Adhikari, Brian M Schwartz, Andrew H Paterson
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents...
February 6, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28166727/whole-genome-sequencing-of-a-plasmodium-vivax-clinical-isolate-exhibits-geographical-characteristics-and-high-genetic-variation-in-china-myanmar-border-area
#14
Shen-Bo Chen, Yue Wang, Kokouvi Kassegne, Bin Xu, Hai-Mo Shen, Jun-Hu Chen
BACKGROUND: Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. RESULTS: The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28155631/a-fast-read-alignment-method-based-on-seed-and-vote-for-next-generation-sequencing
#15
Song Liu, Yi Wang, Fei Wang
BACKGROUND: The next-generation of sequencing technologies, along with the development of bioinformatics, are generating a growing number of reads every day. For the convenience of further research, these reads should be aligned to the reference genome by read alignment tools. Despite the diversity of read alignment tools, most have no comprehensive advantage in both accuracy and speed. For example, BWA has comparatively high accuracy, but its speed leaves much to be desired, becoming a bottleneck while an increasing number of reads need to be aligned every day...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28143409/improved-annotation-with-de-novo-transcriptome-assembly-in-four-social-amoeba-species
#16
Reema Singh, Hajara M Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J Barton, Pauline Schaap, Christian Cole
BACKGROUND: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale...
January 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28123117/phylogenomics-from-whole-genome-sequences-using-atram
#17
Julie M Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I Huang, Patrick G S Grady, Kayce C Bell, Quentin C B Cronk, Lawrence Mugisha, Barry R Pittendrigh, M Soledad Leonardi, David L Reed, Kevin P Johnson
Novel sequencing technologies are rapidly expanding the size of datasets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic datasets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10-30X)...
January 25, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28123114/split-scores-a-tool-to-quantify-phylogenetic-signal-in-genome-scale-data
#18
Elizabeth S Allman, Laura S Kubatko, John A Rhodes
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data become more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and chromosomal inversion are expected to result in changes in the underlying gene trees along a chromosome, while changes in selective pressure and mutational rates for different genomic regions may lead to shifts in the underlying mutational process. We propose the split score as a general method for quantifying support for a particular phylogenetic relationship within a genomic data set...
November 14, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#19
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#20
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
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