scholarly journals ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons

2000 ◽  
Vol 28 (1) ◽  
pp. 267-269 ◽  
Author(s):  
F. Corpet
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Whole Genome ◽  
Genome Comparisons

Whole genome protein domain analysis using a new method for domain clustering

1999 ◽  
Vol 23 (3-4) ◽  
pp. 333-340 ◽  
Author(s):  
Jérome Gouzy ◽  
Florence Corpet ◽  
Daniel Kahn
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
New Method ◽  
Whole Genome

scholarly journals Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection

2016 ◽  
Vol 83 (3) ◽  
Author(s):  
Jean F. Challacombe ◽  
Jeannine M. Petersen ◽  
La Verne Gallegos-Graves ◽  
David Hodge ◽  
Segaran Pillai ◽  
...  
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Response Times ◽  
Amino Acid Sequences ◽  
Clinical Samples ◽  
Whole Genome ◽  
Multiple Gene ◽  
Content Type ◽  
Environmental Surveys ◽  
Genome Comparisons

ABSTRACT Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria. IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.

scholarly journals Whole-Genome k-mer Topic Modeling Associates Bacterial Families

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 197
Author(s):  
Ernesto Borrayo ◽  
Isaias May-Canche ◽  
Omar Paredes ◽  
J. Alejandro Morales ◽  
Rebeca Romo-Vázquez ◽  
...  
Keyword(s):  
Topic Modeling ◽  
Latent Dirichlet Allocation ◽  
Hierarchical Classification ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Comparisons ◽  
Alignment Free ◽  
Biological Phenomena ◽  
Topic Distribution ◽  
Genome Comparisons

Alignment-free k-mer-based algorithms in whole genome sequence comparisons remain an ongoing challenge. Here, we explore the possibility to use Topic Modeling for organism whole-genome comparisons. We analyzed 30 complete genomes from three bacterial families by topic modeling. For this, each genome was considered as a document and 13-mer nucleotide representations as words. Latent Dirichlet allocation was used as the probabilistic modeling of the corpus. We where able to identify the topic distribution among analyzed genomes, which is highly consistent with traditional hierarchical classification. It is possible that topic modeling may be applied to establish relationships between genome’s composition and biological phenomena.

Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

2017 ◽  
Vol 27 (3) ◽  
pp. 147-158 ◽  
Author(s):  
Liliana Godoy ◽  
Evelyn Silva-Moreno ◽  
Wladimir Mardones ◽  
Darwin Guzman ◽  
Francisco A. Cubillos ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Survival Strategies ◽  
Whole Genome ◽  
Biotechnological Applications ◽  
Genome Sequences ◽  
Wine Production ◽  
Brettanomyces Bruxellensis ◽  
Biotechnological Potential ◽  
Spoilage Yeast ◽  
Genome Comparisons

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to <i>Brettanomyces bruxellensis </i>contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 <i>B. bruxellensis </i>annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of <i>B. bruxellensis</i> LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of <i>B. bruxellensis</i> LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of <i>B. bruxellensis</i> LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast <i>B. bruxellensis</i>.

scholarly journals Whole Genome Comparisons Suggest Random Distribution of Mycobacterium ulcerans Genotypes in a Buruli Ulcer Endemic Region of Ghana

2015 ◽  
Vol 9 (3) ◽  
pp. e0003681 ◽  
Author(s):  
Anthony S. Ablordey ◽  
Koen Vandelannoote ◽  
Isaac A. Frimpong ◽  
Evans K. Ahortor ◽  
Nana Ama Amissah ◽  
...  
Keyword(s):  
Random Distribution ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Whole Genome ◽  
Endemic Region ◽  
Genome Comparisons

scholarly journals d-Omix: a mixer of generic protein domain analysis tools

2009 ◽  
Vol 37 (Web Server) ◽  
pp. W417-W421 ◽  
Author(s):  
D. Wichadakul ◽  
S. Numnark ◽  
S. Ingsriswang
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Analysis Tools

scholarly journals Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 129 ◽  
Author(s):  
Sook Jung ◽  
Alessandro Cestaro ◽  
Michela Troggio ◽  
Dorrie Main ◽  
Ping Zheng ◽  
...  
Keyword(s):  
Whole Genome ◽  
Genome Comparisons

scholarly journals The transcriptional regulator pool of the marine bacteriumRhodopirellula balticaSH 1Tas revealed by whole genome comparisons

2005 ◽  
Vol 242 (1) ◽  
pp. 137-145 ◽  
Author(s):  
Thierry Lombardot ◽  
Margarete Bauer ◽  
Hanno Teeling ◽  
Rudolf Amann ◽  
Frank Oliver Glöckner
Keyword(s):  
Transcriptional Regulator ◽  
Whole Genome ◽  
Genome Comparisons

scholarly journals NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

2019 ◽  
Vol 69 (1) ◽  
Author(s):  
Mingzhang Yang ◽  
Myra K. Derbyshire ◽  
Roxanne A. Yamashita ◽  
Aron Marchler‐Bauer
Keyword(s):  
Domain Analysis ◽  
Protein Domain ◽  
Conserved Domain ◽  
Domain Database
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