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JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Michael Richter, Thierry Lombardot, Ivaylo Kostadinov, Renzo Kottmann, Melissa Duhaime, Jörg Peplies, Frank Glöckner
2008 BMC Bioinformatics  
Results: The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes.  ...  Conclusion: JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data.  ...  Acknowledgements We thank Marga Schüler, Stefka Tyanova, Christian Quast, Elmar Prüsse, Anke Meyerdierks, and Beatriz Fernández Gómez for testing the application at early stages of the development and  ... 
doi:10.1186/1471-2105-9-177 pmid:18380896 pmcid:PMC2311307 fatcat:vbdqmtjs6nceril6d4snhltvre

Predominant archaea in marine sediments degrade detrital proteins

Karen G. Lloyd, Lars Schreiber, Dorthe G. Petersen, Kasper U. Kjeldsen, Mark A. Lever, Andrew D. Steen, Ramunas Stepanauskas, Michael Richter, Sara Kleindienst, Sabine Lenk, Andreas Schramm, Bo Barker Jørgensen
2013 Nature  
AB-539-C06 (AOSH00000000), Thermoplasmatales archaeon SCGC AB-539-N05 (ALXL00000000) and Thermoplasmatales archaeon SCGC AB-540-F20  ...  Author Information This whole-genome shotgun project has been deposited at DDBJ/ EMBL/GenBank as Thaumarchaeota archaeon SCGC AB-539-E09 (accession number ALXK00000000), Thermoplasmatales archaeon SCGC  ...  JCoast-A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 9, 177 (2008). 36. Ludwig, W. et al.  ... 
doi:10.1038/nature12033 pmid:23535597 fatcat:wfot6syubzb2biuzmyhuw7rqdq

Assessing the Polysaccharide Degradation Potential in Marine Microbial Genomes and Metagenomes [article]

Sixing Huang, Universität Bremen, Universität Bremen, Rudolf Amann
2020
This doctoral project focuses on CAZyme distributions in marine genomic and metagenomic studies with a focus on the MIMAS (Microbial Interactions in Marine Systems) Project and a sediment sample from the  ...  This limits not only our interpretation of the 'omics (in particular metagenomic) data and understanding of marine ecosystems, but it also keeps us from utilizing this vast enzyme repertoire for biotechnological  ...  Acknowledgements We thank Tobin J Hammer for fruitful discussions and proof reading of the paper.  ... 
doi:10.26092/elib/44 fatcat:qfdecrkxavcotn7kjtrbkuhjhi