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EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Puhler, Frank-Jorg Vorholter, Martha Zakrzewski, Alexander Goesmann
2009 BMC Bioinformatics  
Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes.  ...  Results: To support these studies EDGAR -"Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" -was developed.  ...  The authors further wish to thank the BRF system administrators for expert technical support.  ... 
doi:10.1186/1471-2105-10-154 pmid:19457249 pmcid:PMC2696450 fatcat:wk2r5gvhufginazad346jk4vxu

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva (+2 others)
2016 BMC Bioinformatics  
The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes.  ...  Conclusion: Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories.  ...  The authors thank to Doglas Parise for the help in the conception of the Fig. 2 .  ... 
doi:10.1186/s12859-016-1344-7 pmid:28105921 pmcid:PMC5249034 fatcat:b3daecnlvren3alcbupdqwtj3m

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

Michael A. Skinnider, Chad W. Johnston, Robyn E. Edgar, Chris A. Dejong, Nishanth J. Merwin, Philip N. Rees, Nathan A. Magarvey
2016 Proceedings of the National Academy of Sciences of the United States of America  
The results of a comparative analysis on a large set of genomes suggest that, in addition to introducing unique chemical structure prediction functionality, RiPP-PRISM expands the scope of RiPP genome  ...  A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products.  ... 
doi:10.1073/pnas.1609014113 pmid:27698135 pmcid:PMC5081660 fatcat:eifhtsacxzgwtljrgxjwkofnp4

High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth

Joivier Vichi, Emmanuel Salazar, Verónica Jiménez Jacinto, Leticia Olvera Rodriguez, Ricardo Grande, Edgar Dantán-González, Enrique Morett, Armando Hernández-Mendoza, Juan Mata
2021 PLoS ONE  
In spite of increased complexity in eukaryotes compared to prokaryotes, several basic metabolic and regulatory processes are conserved.  ...  A total of 593 and 860 genes were detected as differentially expressed for E. coli and S. pombe, respectively, with a log2 of the Fold Change ≥ 1 and False Discovery Rate ≤ 0.05.  ...  Cei Abreu Goodger for reviewing and analyzing the data on ncRNAs, Dr. José Díaz for leading the discussion on the  ... 
doi:10.1371/journal.pone.0248513 pmid:33730068 fatcat:uhfmb27hg5akzfvcmv4o3gq73m

Plant ABC proteins – a unified nomenclature and updated inventory

Paul J. Verrier, David Bird, Bo Burla, Elie Dassa, Cyrille Forestier, Markus Geisler, Markus Klein, Üner Kolukisaoglu, Youngsook Lee, Enrico Martinoia, Angus Murphy, Philip A. Rea (+5 others)
2008 Trends in Plant Science  
A consolidated nomenclature will provide much-needed clarity and a framework for future research. 3 The ABC superfamily comprises both membrane-bound transporters and soluble 1 proteins involved in a broad  ...  Completion of the Arabidopsis and rice genome sequences has revealed a particularly large and diverse complement of plant ABC proteins in comparison with other organisms.  ...  naming and clustering 20 of ABC protein components in plant species for which genome sequencing projects 21 are in progress, thus forming a useful starting point for their analysis. 22 FLT is grateful  ... 
doi:10.1016/j.tplants.2008.02.001 pmid:18299247 fatcat:ta7tntlmrrfgdaa5rntztsaa2a

A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited

Tiago M. M. M. Amaro, Gaëtan J. A. Thilliez, Graham B. Motion, Edgar Huitema
2017 Frontiers in Plant Science  
Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across  ...  The increased number of characterized CRNs also has presented a set of challenges that may impede significant progress in the future.  ...  ACKNOWLEDGMENTS The authors would like to thank all the present and past members of the Huitema Laboratory for helpful discussion and suggestions.  ... 
doi:10.3389/fpls.2017.00099 pmid:28217133 pmcid:PMC5289972 fatcat:y3vhwqujdzgbpau3jgwofi3tim

Whole Genome Sequence Comparisons in Taxonomy [chapter]

Rainer Borriss, Christian Rueckert, Jochen Blom, Oliver Bezuidt, Oleg Reva, Hans-Peter Klenk
2011 Methods in Microbiology  
tttttt ACKNOWLEDGEMENTS Long-term financial support for R.B. in frame of the competence network Genome Research on Bacteria (GenoMik, GenoMikPlus and GenMikTransfer) and the Chinese-German collaboration  ...  program by the German Ministry for Education and Research (BMBF) is gratefully acknowledged.  ...  EDGAR EDGAR, another resource for comparative genome analysis, is a dedicated approach for comparative and phylogenetic analysis of closely related genomes.  ... 
doi:10.1016/b978-0-12-387730-7.00018-8 fatcat:vocvwcbghfd3zjh3yz7gamafqy

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI Web site.  ...  TaxPlot plots similarities in the proteomes of two organisms to that of a reference organism for complete prokaryotic and eukaryotic genomes.  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

A Review of Pangenome Tools and Recent Studies [chapter]

G. S. Vernikos
2020 The Pangenome  
With the advance of sequencing technologies, the landscape of genomic analysis has been transformed, by moving from single strain to species (or even higher taxa)-wide genomic resolution, toward the direction  ...  Herein we will review, from practical and technical implementation, existing projects of pangenome analysis, with the aim of providing the reader with a snapshot of useful tools should they need to embark  ...  functional and genomic analysis for a collection of~1300 complete human-associated microbial genomes exploiting a novel dimensionality of analysis that of body site (location of the bug in the human body  ... 
doi:10.1007/978-3-030-38281-0_4 fatcat:pqmpmbqt6fbwdd3k2xwr75icpa

Anti-microbiota vaccines modulate the tick microbiome in a taxon-specific manner [article]

Lourdes Mateos-Hernandez, Dasiel Obregon, Alejandra Wu-Chuang, Jennifer Maye, Jeremie Borneres, Nicolas Versille, Jose de la Fuente, Sandra Diaz, Luis Bermudez-Humaran, Edgar Torres-Maravilla, Agustin Estrada-Pena, Adnan Hodzic (+2 others)
2021 bioRxiv   pre-print
Functional pathways analysis showed that immunization with a live bacterial vaccine can also induce taxon-specific changes in the abundance of pathways.  ...  These results guide interventions for the control of tick infestations and pathogen infection/transmission.  ...  Briefly, the AVSs were placed into 252 a reference tree (NSTI cut-off value of 2) contained 20,000 full 16S rRNA sequences 253 from prokaryotic genomes, which is then used to predict individual gene family  ... 
doi:10.1101/2021.05.12.443756 fatcat:ov5hgqcyqjamxl6pvkkwtnicmu

High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis [article]

Robert Czajkowski, Lukasz Rabalski, Przemyslaw Bartnik, Sylwia Jafra
2021 bioRxiv   pre-print
We believe that the information of this high-quality, complete, closed genome of D. solani strain isolated from host plant different than potato (i.e. hyacinth) will provide resources for comparative genomic  ...  The genome of D. solani strain IPO 2019 consists of one chromosome of 4,919,542 bp., with a GC content of 56.2% and no plasmids.  ...  ., Puhler, A., Vorholter, Zakrzewski, M., and Goesmann, A. 1 2009. EDGAR: A software framework for the comparative analysis of prokaryotic genomes. .  ... 
doi:10.1101/2021.03.02.433526 fatcat:fqowyve76bht3n6hvqxokvq7pq

Inside the Pan-genome - Methods and Software Overview

Luis Carlos Guimaraes, Leandro Benevides de Jesus, Marcus Vinicius Canario Viana, Artur Silva, Rommel Thiago Juca Ramos, Siomar de Castro Soares, Vasco Azevedo
2015 Current Genomics  
has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics.  ...  To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.  ...  EDGAR (Efficient Database Framework for Comparative Genome Analyses Using BLAST Score Ratios) EDGAR is a web-tool (available in: https: //  ... 
doi:10.2174/1389202916666150423002311 pmid:27006628 pmcid:PMC4765519 fatcat:pn6exm2m6ncebgk22o4jyv5cc4

Parallel computing in genomic research: advances and applications

Daniel de Oliveira, Kary Ocaña
2015 Advances and Applications in Bioinformatics and Chemistry  
This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing.  ...  Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes.  ...  Author contributions All authors contributed toward data analysis, drafting and revising the paper and agree to be accountable for all aspects of the work.  ... 
doi:10.2147/aabc.s64482 pmid:26604801 pmcid:PMC4655901 fatcat:qyslams5evftjm7euma5vg2rtq

Ecology, Evolution, and the Genome: A "Whole-Elephant" Reader's Guide

2004 BioScience  
For example, reconstructing a single "tree of life" may be problematic now that comparative genomics has shown horizontal gene transfer to be such a prevalent feature of evolution, at least in prokaryotes  ...  Two recent books are devoted exclusively to the field of comparative genomics, offering complementary perspectives on the analysis of genome evolution.  ... 
doi:10.1641/0006-3568(2004)054[0950:eeatga];2 fatcat:jgdvetivb5ailpq46r27fxbhdu

An Assessment of the Impacts of Molecular Oxygen on the Evolution of Proteomes

S. Vieira-Silva, E. P. C. Rocha
2008 Molecular biology and evolution  
Many proteome adaptations have been proposed to tackle such stresses and we assessed them using comparative genomics in a phylogenetic context.  ...  Accordingly, we find no evidence of oxygen being a scarce resource for protein synthesis even among anaerobes.  ...  We thank Isabelle Gonc xalves, Antoine Danchin, and Guillaume Santini for criticisms, comments, and suggestions on previous versions of this manuscript and Antoine Danchin for pointing to us the hypothesis  ... 
doi:10.1093/molbev/msn142 pmid:18579552 pmcid:PMC2515869 fatcat:3pduxavgpjhwhkz24gjc7dlfum
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