Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams

2017 ◽  
pp. 239-260 ◽  
Author(s):  
Dann Turner ◽  
J. Mark Sutton ◽  
Darren M. Reynolds ◽  
Eby M. Sim ◽  
Nicola K. Petty
Keyword(s):  
Comparative Genomics ◽  
Genomic Data ◽  
Publication Quality

scholarly journals MOSGA 2: Comparative genomics and validation tools

2021 ◽  
Author(s):  
Roman Martin ◽  
Hagen Dreßler ◽  
Georges Hattab ◽  
Thomas Hackl ◽  
Matthias G Fischer ◽  
...  
Keyword(s):  
Quality Control ◽  
Comparative Genomics ◽  
Data Quality ◽  
Genomic Data ◽  
Data Sets ◽  
Genomic Information ◽  
High Quality ◽  
Genome Annotations ◽  
Genome Assemblies ◽  
Annotation Quality

Due to the highly growing number of available genomic information, the need for accessible and easy-to-use analysis tools is increasing. To facilitate eukaryotic genome annotations, we created MOSGA. In this work, we show how MOSGA~2 is developed by including several advanced analyses for genomic data. Since the genomic data quality greatly impacts the annotation quality, we included multiple tools to validate and ensure high-quality user-submitted genome assemblies. Moreover, thanks to the integration of comparative genomics methods, users can benefit from a broader genomic view by analyzing multiple genomic data sets simultaneously. Further, we demonstrate the new functionalities of MOSGA~2 by different use-cases and practical examples. MOSGA~2 extends the already established application to the quality control of the genomic data and integrates and analyzes multiple genomes in a larger context, e.g., by phylogenetics.

scholarly journals Complete and Draft Genome Sequences of 12 Plant-Associated Rathayibacter Strains of Known and Putative New Species

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Sergey V. Tarlachkov ◽  
Irina P. Starodumova ◽  
Lubov V. Dorofeeva ◽  
Natalia V. Prisyazhnaya ◽  
Semen A. Leyn ◽  
...  
Keyword(s):  
New Species ◽  
Comparative Genomics ◽  
Genomic Dna ◽  
Draft Genome ◽  
Genomic Data ◽  
Genome Sequences ◽  
Oxford Nanopore ◽  
Baseline Information

ABSTRACT Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter.

scholarly journals Ensembl 2021

2020 ◽  
Vol 49 (D1) ◽  
pp. D884-D891 ◽  
Author(s):  
Kevin L Howe ◽  
Premanand Achuthan ◽  
James Allen ◽  
Jamie Allen ◽  
Jorge Alvarez-Jarreta ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Genomic Data ◽  
Regulatory Elements ◽  
Vertebrate Species ◽  
Variant Effect Predictor ◽  
Rapid Release ◽  
History Of ◽  
Genome Browsers ◽  
Gene Structures

Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

scholarly journals Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

2019 ◽  
Author(s):  
Galo A. Goig ◽  
Manuela Torres-Puente ◽  
Carla Mariner-Llicer ◽  
Luis M. Villamayor ◽  
Álvaro Chiner-Oms ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
Causes Of Death ◽  
Molecular Targets ◽  
Genomic Data ◽  
Clinical Samples ◽  
Physiological Status ◽  
Molecular Tools ◽  
Public Health Agencies ◽  
Health Agencies

AbstractTuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturingMycobacterium tuberculosiscomplex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that are unique to the MTBC. Some of these genes could be targeted to assess the physiological status of the bacilli. Remarkably, none of the conventional MTBC markers is in our catalog. In addition, we develop a qPCR assay to accurately quantify MTBC DNA in clinical samples.

scholarly journals Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii and C. flaccumfaciens pv. poinsettiae

2022 ◽  
Author(s):  
Ebrahim Osdaghi ◽  
Geraldine Taghouti ◽  
Cecile Dutrieux ◽  
S. Mohsen Taghavi ◽  
Amal Fazliarab ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Ornamental Plants ◽  
Genomic Data ◽  
Economic Importance ◽  
Whole Genome Sequence ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Complex Species ◽  
Annual Crops ◽  
The Family

Curtobacterium flaccumfaciens complex species in the family Microbacteriaceae encompasses a group of plant pathogenic actinobacterial strains affecting annual crops and ornamental plants. The species includes five pathovars namely C. flaccumfaciens pv. betae, C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. ilicis, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Despite the economic importance of C. flaccumfaciens, its members have rarely been investigated for their phylogenetic relationships, molecular characteristics and virulence repertories due in part to the lack of whole genome resources. Here we present the whole genome sequence of 17 C. flaccumfaciens strains representing members of four pathovars isolated from different plant species in a diverse geographical and temporal span. The genomic data presented in this study will pave the way of research on the comparative genomics, phylogenomics and taxonomy of C. flaccumfaciens, and extend our understanding of the virulence features of the species.

scholarly journals VIVA (VIsualization of VAriants): A VCF file visualization tool

2019 ◽  
Author(s):  
George A. Tollefson ◽  
Jessica Schuster ◽  
Fernando Gelin ◽  
Ashok Ragavendran ◽  
Isabel Restrepo ◽  
...  
Keyword(s):  
Biological Sciences ◽  
High Throughput Sequencing ◽  
Genomic Data ◽  
Visualization Tool ◽  
Variant Call Format ◽  
Variant Call ◽  
Technological Advances ◽  
Sequencing Studies ◽  
User Friendly ◽  
Publication Quality

ABSTRACTThe volume and pace of data accumulation from high-throughput sequencing studies have been amplified by recent rapid technological advances in biological sciences. Visualization of genomic data is essential for quality control, exploration, and interpretation. Here, we describe a user-friendly visualization tool for variant call format (VCF) files with which the users can interactively evaluate and share genomic data, as well as create publication quality graphics.

Small Computer System for Micrograph Analysis

1981 ◽  
Vol 39 ◽  
pp. 270-271
Author(s):  
J. F. Hainfeld ◽  
J. S. Wall
Keyword(s):  
Large Range ◽  
Small Computer ◽  
Black And White ◽  
Contour Maps ◽  
Points Of Interest ◽  
Computer Aided Analysis ◽  
Specialized Hardware ◽  
Additional Memory ◽  
Selection Of ◽  
Publication Quality

Cost reduction and availability of specialized hardware for image processing have made it reasonable to purchase a stand-alone interactive work station for computer aided analysis of micrographs. Some features of such a system are: 1) Ease of selection of points of interest on the micrograph. A cursor can be quickly positioned and coordinates entered with a switch. 2) The image can be nondestructively zoomed to a higher magnification for closer examination and roaming (panning) can be done around the picture. 3) Contrast and brightness of the picture can be varied over a very large range by changing the display look-up tables. 4) Marking items of interest can be done by drawing circles, vectors or alphanumerics on an additional memory plane so that the picture data remains intact. 5) Color pictures can easily be produced. Since the human eye can detect many more colors than gray levels, often a color encoded micrograph reveals many features not readily apparent with a black and white display. Colors can be used to construct contour maps of objects of interest. 6) Publication quality prints can easily be produced by taking pictures with a standard camera of the T.V. monitor screen.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

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