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Whole genome alignment

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https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#1
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Background: Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28423505/identification-and-analysis-of-mutational-hotspots-in-oncogenes-and-tumour-suppressors
#2
Hanadi Baeissa, Graeme Benstead-Hume, Christopher J Richardson, Frances M G Pearl
BACKGROUND: The key to interpreting the contribution of a disease-associated mutation in the development and progression of cancer is an understanding of the consequences of that mutation both on the function of the affected protein and on the pathways in which that protein is involved. Protein domains encapsulate function and position-specific domain based analysis of mutations have been shown to help elucidate their phenotypes. RESULTS: In this paper we examine the domain biases in oncogenes and tumour suppressors, and find that their domain compositions substantially differ...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420412/intersect-then-combine-approach-improving-the-performance-of-somatic-variant-calling-in-whole-exome-sequencing-data-using-multiple-aligners-and-callers
#3
Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M Rueda, Suet-Feung Chin, Carlos Caldas
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28398543/funchip-an-r-bioconductor-package-for-functional-classification-of-chip-seq-shapes
#4
Alice C L Parodi, Laura M Sangalli, Simone Vantini, Bruno Amati, Piercesare Secchi, Marco J Morelli
Summary: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimises their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28392341/computational-complexity-of-algorithms-for-sequence-comparison-short-read-assembly-and-genome-alignment
#5
REVIEW
Shakuntala Baichoo, Christos A Ouzounis
A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience...
April 6, 2017: Bio Systems
https://www.readbyqxmd.com/read/28369524/ngscheckmate-software-for-validating-sample-identity-in-next-generation-sequencing-studies-within-and-across-data-types
#6
Sejoon Lee, Soohyun Lee, Scott Ouellette, Woong-Yang Park, Eunjung A Lee, Peter J Park
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369270/dltree-efficient-and-accurate-phylogeny-reconstruction-using-the-dynamical-language-method
#7
Qi Wu, Zu-Guo Yu, Jianyi Yang
Summary: A number of alignment-free methods have been proposed for phylogeny reconstruction over the past two decades. But there are some long-standing challenges in these methods, including requirement of huge computer memory and CPU time, and existence of duplicate computations. In this article, we address these challenges with the idea of compressed vector, fingerprint and scalable memory management. With these ideas we developed the DLTree algorithm for efficient implementation of the dynamical language model and whole genome-based phylogenetic analysis...
March 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28361696/p-hint-hunt-a-deep-parallelized-whole-genome-dna-methylation-detection-tool
#8
Shaoliang Peng, Shunyun Yang, Ming Gao, Xiangke Liao, Jie Liu, Canqun Yang, Chengkun Wu, Wenqiang Yu
BACKGROUND: The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and several typical diseases, such as cancers and diabetes. In many of those studies, mapping the bisulfite treated sequence to the whole genome has been the main method to study DNA cytosine methylation. However, today's relative tools almost suffer from inaccuracies and time-consuming problems...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28351369/positional-bias-in-variant-calls-against-draft-reference-assemblies
#9
Roman V Briskine, Kentaro K Shimizu
BACKGROUND: Whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. Despite lower quality of such assemblies, they allowed researchers to extend a wide range of population genetic and genome-wide association analyses to non-model species. As the variant calling pipelines are complex and involve many software packages, it is important to understand inherent biases and limitations at each step of the analysis...
March 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28348869/nasp-an-accurate-rapid-method-for-the-identification-of-snps-in-wgs-datasets-that-supports-flexible-input-and-output-formats
#10
Jason W Sahl, Darrin Lemmer, Jason Travis, James M Schupp, John D Gillece, Maliha Aziz, Elizabeth M Driebe, Kevin P Drees, Nathan D Hicks, Charles Hall Davis Williamson, Crystal M Hepp, David Earl Smith, Chandler Roe, David M Engelthaler, David M Wagner, Paul Keim
Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset...
August 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28348851/snp-sites-rapid-efficient-extraction-of-snps-from-multi-fasta-alignments
#11
Andrew J Page, Ben Taylor, Aidan J Delaney, Jorge Soares, Torsten Seemann, Jacqueline A Keane, Simon R Harris
Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis...
April 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28347645/evolution-of-the-vertebrate-phototransduction-cascade-activation-steps
#12
Trevor D Lamb, David M Hunt
We examine the molecular phylogeny of the proteins underlying the activation steps of vertebrate phototransduction, for both agnathan and jawed vertebrate taxa. We expand the number of taxa analysed and we update the alignment and tree building methodology from a previous analysis. For each of the four primary components (the G-protein transducin alpha subunit, GαT, the cyclic GMP phosphodiesterase, PDE6, and the alpha and beta subunits of the cGMP-gated ion channel, CNGC), the phylogenies appear consistent with expansion from an ancestral proto-vertebrate cascade during two rounds of whole-genome duplication followed by divergence of the agnathan and jawed vertebrate lineages...
March 24, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28344774/the-dockstore-enabling-modular-community-focused-sharing-of-docker-based-genomics-tools-and-workflows
#13
Brian D O'Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing...
2017: F1000Research
https://www.readbyqxmd.com/read/28334120/svpv-a-structural-variant-prediction-viewer-for-paired-end-sequencing-datasets
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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...
April 2017: Human Immunology
https://www.readbyqxmd.com/read/28258183/the-bacterial-sequential-markov-coalescent
#20
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
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