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https://www.readbyqxmd.com/read/28527624/understanding-aerobic-anaerobic-metabolism-in-caldibacillus-debilis-through-a-comparison-with-model-organisms
#1
Scott Wushke, Victor Spicer, Xiang Li Zhang, Brian Fristensky, Oleg V Krokhin, David B Levin, Nazim Cicek, Richard Sparling
Caldibacillus debilis GB1 is a facultative anaerobe isolated from a thermophilic aero-tolerant cellulolytic enrichment culture. There is a lack of representative proteomes of facultative anaerobic thermophilic Bacillaceae, exploring aerobic/anaerobic expression. The C. debilis GB1 genome was sequenced and annotated, and the proteome characterized under aerobic and anaerobic conditions while grown on cellobiose. The draft sequence of C. debilis GB1 contains a 3,340,752 bp chromosome and a 5,386 bp plasmid distributed over 49 contigs...
April 13, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28526988/identification-of-candidate-genes-for-paratuberculosis-resistance-in-the-native-italian-garfagnina-goat-breed
#2
Francesca Cecchi, Claudia Russo, Daniela Iamartino, Alessia Galiero, Barbara Turchi, Filippo Fratini, Sara Degl'Innocenti, Raffaele Mazza, Stefano Biffani, Giovanna Preziuso, Carlo Cantile
Paratuberculosis disease is a chronic bacterial disease infection of ruminants of global relevance, caused by MAP (Mycobacterium avium subsp. paratuberculosis). The present study was conducted on the Garfagnina goat breed that is an Italian native goat population registered on the Tuscan regional repertory of genetic resources at risk of extinction. Forty-eight adult goats (27 serologically positive to MAP-positive and 21 serologically negative to MAP-negative) belonging to a single flock that had experienced annual mortalities due to MAP infection were identified and genotyped with the Illumina GoatSNP60 BeadChip...
May 19, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28526965/complete-sequence-and-genomic-annotation-of-carrot-torradovirus-1
#3
Zuriñe Rozado-Aguirre, Ian Adams, Adrian Fox, Matthew Dickinson, Neil Boonham
Carrot torradovirus 1 (CaTV1) is a new member of the genus Torradovirus within the family Secoviridae. CaTV1 genome sequences were obtained from a previous next-generation sequencing (NGS) study and were compared to other members and tentative new members of the genus. The virus has a bipartite genome, and RACE was used to amplify and sequence each end of RNA1 and RNA2. As a result, RNA1 and RNA2 are estimated to contain 6944 and 4995 nucleotides, respectively, with RNA1 encoding the proteins involved in virus replication, and RNA2 encoding the encapsidation and movement proteins...
May 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28526730/a-targeted-capture-linkage-map-anchors-the-genome-of-the-schistosomiasis-vector-snail-biomphalaria-glabrata
#4
Jacob A Tennessen, Stephanie R Bollmann, Michael S Blouin
The aquatic planorbid snail Biomphalaria glabrate is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here we used targeted capture markers to map over 10,000 B. glabrate scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups. We added additional scaffolds to these linkage groups based on linkage disequilibrium analysis of targeted capture and whole-genome sequences of 96 unrelated snails...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526573/transcriptomic-variation-of-locally-infected-skin-of-epinephelus-coioides-reveals-the-mucosal-immune-mechanism-against-cryptocaryon-irritans
#5
Yazhou Hu, Anxing Li, Yang Xu, Biao Jiang, Geling Lu, Xiaochun Luo
Fish skin is the largest immunologically active mucosal organ, providing first-line defense against external pathogens. However, the skin-associated immune mechanisms of fish are still unclear. Cryptocaryon irritans is an obligate ectoparasitic ciliated protozoan that infects almost all marine fish, and is believed to be an excellent pathogen model to study fish mucosal immunity. In this study, a de novo transcriptome assembly of Epinephelus coioides skin post C. irritans tail-infection was performed for the first time using the Illumina HiSeq™ 2500 system...
May 16, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28525966/gene-expression-of-vibrio-parahaemolyticus-growing-in-laboratory-isolation-conditions-compared-to-those-common-in-its-natural-ocean-environment
#6
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525531/phyd3-a-phylogenetic-tree-viewer-with-extended-phyloxml-support-for-functional-genomics-data-visualization
#7
Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele, Michiel Van Bel
Motivation: Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise biological data. Recently, several web-based tools for the display, manipulation, and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available...
May 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#8
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28523007/transcriptomic-identification-of-drought-related-genes-and-ssr-markers-in-sudan-grass-based-on-rna-seq
#9
Yongqun Zhu, Xia Wang, Linkai Huang, Chaowen Lin, Xinquan Zhang, Wenzhi Xu, Jianhua Peng, Zhou Li, Haidong Yan, Fuxiang Luo, Xie Wang, Li Yao, Dandan Peng
Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#10
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28521726/orthofiller-utilising-data-from-multiple-species-to-improve-the-completeness-of-genome-annotations
#11
Michael P Dunne, Steven Kelly
BACKROUND: Complete and accurate annotation of sequenced genomes is of paramount importance to their utility and analysis. Differences in gene prediction pipelines mean that genome annotations for a species can differ considerably in the quality and quantity of their predicted genes. Furthermore, genes that are present in genome sequences sometimes fail to be detected by computational gene prediction methods. Erroneously unannotated genes can lead to oversights and inaccurate assertions in biological investigations, especially for smaller-scale genome projects, which rely heavily on computational prediction...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#12
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28518075/leveraging-cyverse-resources-for-de-novo-comparative-transcriptomics-of-underserved-non-model-organisms
#13
Blake L Joyce, Asher K Haug-Baltzell, Jonathan P Hulvey, Fiona McCarthy, Upendra Kumar Devisetty, Eric Lyons
This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g. executing bash commands, visualization and management of large data sets. All command line code and further explanations of each command or step can be found on the wiki (https://wiki.cyverse.org/wiki/x/dgGtAQ). The Discovery Environment and Atmosphere platforms are connected together through the CyVerse Data Store...
May 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28516912/a-complete-tool-set-for-molecular-qtl-discovery-and-analysis
#14
Olivier Delaneau, Halit Ongen, Andrew A Brown, Alexandre Fort, Nikolaos I Panousis, Emmanouil T Dermitzakis
Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple new and well-established methods to prepare the data, to discover proximal and distal molQTLs and, finally, to integrate them with GWAS variants and functional annotations of the genome...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28516383/genetic-analysis-of-the-lf1-gene-that-controls-leaflet-number-in-soybean
#15
Soon-Chun Jeong, Ji Hong Kim, Dong Nyuk Bae
A high-resolution genetic map that was constructed for the Lf1 -residing region will provide valuable information for map-based cloning and genetic improvement efforts in soybean. Changes in leaf architecture as photosynthesis factories remain a major challenge for the improvement of crop productivity. Unlike most soybeans, which have compound leaves comprising three leaflets, the soybean Lf1 mutant has a high frequency of compound leaves with five leaflets in a partially dominant manner. Here, we generated a fine genetic map to determine the genetic basis of this multifoliolate leaf trait...
May 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28515914/analysis-of-the-function-of-microrna-375-in-humans-using-bioinformatics
#16
Xiaohua Chen, Baoxia Li, Rongcheng Luo, Sina Cai, Cao Zhang, Xiaolong Cao
MicroRNA-375 (miR-375) is expressed at low levels in many types of solid tumor, particularly in gastrointestinal tumors. It is considered to be important in the development of cancer and certain diseases. Thus, more detailed knowledge is required on the particular functions of miR-375. miRs function by regulating target genes. Therefore, in the current study, miRWalk (which includes the data from 10 prediction software programs) was used to predict the target genes of miR-375. The genes, which were co-predicted using five different software programs were further analyzed using Database for Annotation, Visualization and Integrated Discovery online software [including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis]...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#17
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28514442/architecture-of-the-human-interactome-defines-protein-communities-and-disease-networks
#18
Edward L Huttlin, Raphael J Bruckner, Joao A Paulo, Joe R Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E White, Devin K Schweppe, Ramin Rad, Brian K Erickson, Robert A Obar, K G Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P Gygi, J Wade Harper
The physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28512992/association-of-cd8-t-cells-with-bone-erosion-in-patients-with-rheumatoid-arthritis
#19
Young Bin Joo, Youngho Park, Kwangwoo Kim, So-Young Bang, Sang-Cheol Bae, Hye-Soon Lee
AIM: Bone erosion is a major problem worsening quality of rheumatoid arthritis (RA) patients' lives. However, causal factors responsible for bone erosion in RA have remained unclear. We aimed to examine genetic variants conferring bone erosion in RA using a Korean genome-wide association study (GWAS) and to search for possible biological mechanisms underlying the development of bone erosion. METHOD: We obtained genome-wide single nucleotide polymorphism (SNP) data for 711 Korean RA patients using Illumina HapMap 550v3/660W arrays...
May 16, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28509971/description-of-chryseobacterium-timonianum-sp-nov-isolated-from-a-patient-with-pneumonia
#20
Rita Abou Abdallah, Teresa Cimmino, Sophie Baron, Frédéric Cadoret, Caroline Michelle, Didier Raoult, Pierre-Edouard Fournier, Fadi Bittar
Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972(T), could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777(T), the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species...
May 16, 2017: Antonie Van Leeuwenhoek
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