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Whole genome alignment

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https://www.readbyqxmd.com/read/28541377/asap-a-web-based-platform-for-the-analysis-and-interactive-visualization-of-single-cell-rna-seq-data
#1
Vincent Gardeux, Fabrice P A David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke
Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often lack the expertise to handle complex scRNA-seq data sets. Results: We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28539120/comprehensive-whole-genome-sequence-analyses-yields-novel-genetic-and-structural-insights-for-intellectual-disability
#2
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, Madeline Couse, Karen L Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F Boerkoel, Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BACKGROUND: Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS: We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525288/inference-of-the-genetic-polymorphisms-of-cyp2d6-in-six-subtribes-of-the-malaysian-orang-asli-from-whole-genome-sequencing-data
#3
Choo Yee Yu, Geik Yong Ang, Vinothini Subramaniam, Richard Johari James, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor, Syahrul Azlin Shaari, Lay Kek Teh, Mohd Zaki Salleh
AIMS: CYP2D6 is one of the major enzymes in the cytochrome P450 monooxygenase system. It metabolizes ∼25% of prescribed drugs and hence, the genetic diversity of CYP2D6 gene has continued to be of great interest to the medical and pharmaceutical industries. This study aims to perform a systematic analysis of the CYP2D6 gene in six subtribes of the Malaysian Orang Asli. METHODS: Genomic DNAs were extracted from the blood samples followed by whole-genome sequencing...
May 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28511677/a-strategy-to-improve-phasing-of-whole-genome-sequenced-individuals-through-integration-of-familial-information-from-dense-genotype-panels
#4
Pierre Faux, Tom Druet
BACKGROUND: Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) information. With whole-genome sequence (WGS) data, relatively small samples of reference individuals are generally sequenced due to prohibitive sequencing costs, thus only a limited amount of familial information is available. However, reference individuals have many relatives that have been genotyped (at lower density)...
May 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#5
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28492527/single-cell-template-strand-sequencing-by-strand-seq-enables-the-characterization-of-individual-homologs
#6
Ashley D Sanders, Ester Falconer, Mark Hills, Diana C J Spierings, Peter M Lansdorp
The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28486572/evaluation-of-mc1r-high-throughput-nucleotide-sequencing-data-generated-by-the-1000-genomes-project
#7
Leonardo Arduino Marano, Letícia Marcorin, Erick da Cruz Castelli, Celso Teixeira Mendes-Junior
The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology...
May 8, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28481935/genotypic-and-phenotypic-characterization-of-multidrug-resistant-salmonella-typhimurium-and-salmonella-kentucky-strains-recovered-from-chicken-carcasses
#8
Rizwana Tasmin, Nur A Hasan, Christopher J Grim, Ar'Quette Grant, Seon Young Choi, M Samiul Alam, Rebecca Bell, Christopher Cavanaugh, Kannan V Balan, Uma S Babu, Salina Parveen
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28473773/analyses-of-mmp20-missense-mutations-in-two-families-with-hypomaturation-amelogenesis-imperfecta
#9
Youn Jung Kim, Jenny Kang, Figen Seymen, Mine Koruyucu, Koray Gencay, Teo Jeon Shin, Hong-Keun Hyun, Zang Hee Lee, Jan C-C Hu, James P Simmer, Jung-Wook Kim
Amelogenesis imperfecta is a group of rare inherited disorders that affect tooth enamel formation, quantitatively and/or qualitatively. The aim of this study was to identify the genetic etiologies of two families presenting with hypomaturation amelogenesis imperfecta. DNA was isolated from peripheral blood samples obtained from participating family members. Whole exome sequencing was performed using DNA samples from the two probands. Sequencing data was aligned to the NCBI human reference genome (NCBI build 37...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28453674/ntcard-a-streaming-algorithm-for-cardinality-estimation-in-genomics-data
#10
Hamid Mohamadi, Hamza Khan, Inanc Birol
Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449639/clovr-comparative-automated-cloud-enabled-comparative-microbial-genome-sequence-analysis-pipeline
#11
Sonia Agrawal, Cesar Arze, Ricky S Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M Fraser, Hervé Tettelin, Owen White, Samuel V Angiuoli, Anup Mahurkar, W Florian Fricke
BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI...
April 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28442399/the-genome-sequence-of-agrotis-segetum-granulovirus-isolate-agsegv-da-reveals-a-new-betabaculovirus-species-of-a-slow-killing-granulovirus
#12
Gianpiero Gueli Alletti, Marina Eigenbrod, Eric B Carstens, Regina G Kleespies, Johannes A Jehle
The European isolate Agrotis segetum granulovirus DA (AgseGV-DA) is a slow killing, type I granulovirus due to low dose-mortality responses within seven days post infection and a tissue tropism of infection restricted solely to the fat body of infected Agrotis segetum host larvae. The genome of AgseGV-DA was completely sequenced and compared to the whole genome sequences of the Chinese isolates AgseGV-XJ and AgseGV-L1. All three isolates share highly conserved genomes. The AgseGV-DA genome is 131,557bp in length and encodes for 149 putative open reading frames, including 37 baculovirus core genes and the per os infectivity factor ac110...
April 22, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28438488/whole-genome-sequencing-predicts-novel-human-disease-models-in-rhesus-macaques
#13
Benjamin N Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M Peterson, Robert B Norgren, Betsy Ferguson
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model...
April 23, 2017: Genomics
https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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