scholarly journals Whole-Genome Analysis of Halomonas sp. Soap Lake #7 Reveals It Possesses Putative Mrp Antiporter Operon Groups 1 and 2

2019 ◽  
Vol 11 (6) ◽  
pp. 1706-1709 ◽  
Author(s):  
Melanie R Mormile ◽  
Tiffany Edwards ◽  
Ron Frank ◽  
Zachery Geurin ◽  
Julie Haendiges ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Multiple Resistance ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
First Report ◽  
Ph Tolerance ◽  
Wide Range ◽  
Group 2 ◽  
Soap Lake ◽  
Group 1

Abstract The genus Halomonas possesses bacteria that are halophilic or halotolerant and exhibit a wide range of pH tolerance. The genome of Halomonas sp. Soap Lake #7 was sequenced to provide a better understanding of the mechanisms for salt and pH tolerance in this genus. The bacterium’s genome was found to possess two complete multiple resistance and pH antiporter systems, Group 1 and Group 2. This is the first report of both multiple resistance and pH antiporter Groups 1 and 2 in the genome of a haloalkaliphilic bacterium.

scholarly journals GAAP: A Genome Assembly + Annotation Pipeline

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Jinhwa Kong ◽  
Sun Huh ◽  
Jung-Im Won ◽  
Jeehee Yoon ◽  
Baeksop Kim ◽  
...  
Keyword(s):  
Genome Analysis ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Analysis ◽  
Whole Genome ◽  
High Throughput Analysis ◽  
Whole Genome Analysis ◽  
A Genome ◽  
Base Sequences ◽  
Wide Range

Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method.

scholarly journals Whole-genome analysis uncovers loss of blaZ associated to carriage isolates belonging to MRSA clone ST5-VI in Cape Verde

2021 ◽  
Author(s):  
Magdalena Wysocka ◽  
Tamar Monteiro ◽  
Carine de Pina ◽  
Deisy Gonçalves ◽  
Sandrine de Pina ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Cape Verde ◽  
Whole Genome ◽  
Whole Genome Analysis

Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

2007 ◽  
Vol 9 (12) ◽  
pp. 2993-3007 ◽  
Author(s):  
Lisa Y. Stein ◽  
Daniel J. Arp ◽  
Paul M. Berube ◽  
Patrick S. G. Chain ◽  
Loren Hauser ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Niche Adaptation ◽  
Ammonia Oxidizing Bacterium

scholarly journals Whole-Genome Analysis of Oryza sativa Reveals Similar Architecture of Two-Component Signaling Machinery with Arabidopsis

2006 ◽  
Vol 142 (2) ◽  
pp. 380-397 ◽  
Author(s):  
Ashwani Pareek ◽  
Anupama Singh ◽  
Manoj Kumar ◽  
Hemant R. Kushwaha ◽  
Andrew M. Lynn ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Two Component

scholarly journals The cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers

2017 ◽  
Vol 5 (3) ◽  
pp. 251-260 ◽  
Author(s):  
Deirdre Weymann ◽  
Janessa Laskin ◽  
Robyn Roscoe ◽  
Kasmintan A. Schrader ◽  
Stephen Chia ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
The Cost
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