scholarly journals Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale

2002 ◽  
Vol 30 (24) ◽  
pp. 5382-5390 ◽  
Author(s):  
O. Lecompte
Keyword(s):  
Comparative Analysis ◽  
Ribosomal Proteins ◽  
Reductive Evolution ◽  
Complete Genomes

scholarly journals CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

2007 ◽  
Vol 36 (Supplement_1) ◽  
pp. D504-D511 ◽  
Author(s):  
Yi Huang ◽  
Susanna K. P. Lau ◽  
Patrick C. Y. Woo ◽  
Kwok-yung Yuen
Keyword(s):  
Comparative Analysis ◽  
Comparative Sequence Analysis ◽  
Nomenclature System ◽  
Comprehensive Database ◽  
Representative Sequence ◽  
Phylogenetic Studies ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Bat Coronavirus ◽  
Group 1

Abstract The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.

scholarly journals The archaeal origins of the eukaryotic translational system

Archaea ◽  
2006 ◽  
Vol 2 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Hyman Hartman ◽  
Paola Favaretto ◽  
Temple F. Smith
Keyword(s):  
Comparative Analysis ◽  
Host Cell ◽  
Ribosomal Proteins ◽  
Phylogenetic Analyses ◽  
Substantial Fraction ◽  
Translational Machinery ◽  
Prokaryotic Diversity ◽  
Srp Rna ◽  
Modern Sense

Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea. Several other translational proteins are common only to Eukarya and Archaea (e.g., IF2a, SRP19, etc.), whereas others are shared by the three phyla (e.g., EFTu/EF1A and SRP54).Although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translational machinery, especially the ribosomal proteins, there have been numerous unique and ubiquitous additions to the eukaryotic translational system besides the 11 unique eukaryotic ribosomal proteins. These include peptide additions to most of the 67 archaeal homolog proteins, rRNA insertions, the 5.8S RNA and the Alu extension to the SRP RNA. Our comparative analysis of these and other eukaryotic features among the three different cellular phylodomains supports the idea that an archaeal translational system was most likely incorporated by means of endosymbiosis into a host cell that was neither bacterial nor archaeal in any modern sense. Phylogenetic analyses provide support for the timing of this acquisition coinciding with an ancient bottleneck in prokaryotic diversity.

scholarly journals In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis

2019 ◽  
Vol 11 (2) ◽  
pp. 80-87
Author(s):  
N. P. Peretolchina ◽  
Yu. P. Dzhioev ◽  
A. Yu. Borisenko ◽  
L. A. Stepanenko ◽  
E. A. Voskresenskaya ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Yersinia Pseudotuberculosis ◽  
Protein Structures ◽  
Clinical Manifestations ◽  
Systemic Infection ◽  
Complete Genomes ◽  
Nucleotide Database ◽  
Cas Genes ◽  
Species Variability ◽  
Cas Proteins

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

Comparative analysis of human papillomavirus type 6 complete genomes originated from head and neck and anogenital disorders

2019 ◽  
Vol 71 ◽  
pp. 140-150
Author(s):  
Mihály Szinai ◽  
Zsófia Nagy ◽  
Petra Máté ◽  
Dávid Kovács ◽  
Levente Laczkó ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Comparative Analysis ◽  
Head And Neck ◽  
Complete Genomes

scholarly journals Variant analysis of 1,040 SARS-CoV-2 genomes

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241535 ◽  
Author(s):  
Eric C. Rouchka ◽  
Julia H. Chariker ◽  
Donghoon Chung
Keyword(s):  
Comparative Analysis ◽  
Viral Genome ◽  
Untranslated Region ◽  
Rna Virus ◽  
Population Analysis ◽  
Whole Genome ◽  
Coding Sequences ◽  
Complete Genomes ◽  
Intergenic Regions ◽  
Variant Analysis

The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within the 3’UTR, 2 within intergenic regions and 34 within coding sequences.

A Novel Complexity Measure for Comparative Analysis of Protein Sequences from Complete Genomes

2003 ◽  
Vol 20 (5) ◽  
pp. 657-667 ◽  
Author(s):  
Tannistha Nandi ◽  
Debasis Dash ◽  
Rohit Ghai ◽  
Chandrika B-Rao ◽  
K. Kannan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Protein Sequences ◽  
Complexity Measure ◽  
Complete Genomes

Genetic characterization of enterovirus 71 isolated from patients with severe disease by comparative analysis of complete genomes

2012 ◽  
Vol 84 (6) ◽  
pp. 931-939 ◽  
Author(s):  
Shih-Cheng Chang ◽  
Wen-Chen Li ◽  
Guang-Wu Chen ◽  
Kuo-Chien Tsao ◽  
Chung-Guei Huang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Characterization ◽  
Severe Disease ◽  
Enterovirus 71 ◽  
Complete Genomes
Sign in / Sign up

Export Citation Format

Share Document