Improving the Usage of ribosomal RNA Gene in Microbiology and Microbial Ecology Importance of Standardization and Biocuration

  • Environmental surveys of ribosomal RNA genes have become the standard approach to microbial ecology in the last twenty-five years. Although the ribosomal RNA approach has been competing with metagenomics during the past years, with high-throughput sequencing technologies presenting the ability to document the diversity and richness of the microbial biome at an astonishing rate, it is once again under spotlight. High-throughput sequencing technologies bring with them a sequence data deluge, and present challenges to the traditional data management, analysis and retrieval practices. Biocuration, which leads to specialized ribosomal RNA datasets, has become an important part of microbial ecology. More recently, the development and use of metadata standards has emerged as an important aid for biocuration in microbiology. With the help of such standards, it will be possible to curate specialized datasets, which integrate data from even more diverse resources, and bring the organisms, its functions, and the environment together. The work accomplished during this Ph.D. thesis aimed in improving the usage of ribosomal RNA gene in microbiology and microbial ecology by means of curating highquality specialized datasets for ribosomal RNA gene sequences, and performing research that demonstrates the value of such datasets. More importantly, a metadata standard for marker genes sequences, such as ribosomal RNA, was developed and disseminated to a variety of bioinformatics service providers for implementation. This standard will greatly aid biocuration work in microbiology, and will improve the quantity and quality of integrative resources for microbiology, ultimately providing researchers the ability to understand the diversity and functioning of the microbial biosphere.

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Publishing Institution:IRC-Library, Information Resource Center der Jacobs University Bremen
Granting Institution:Jacobs Univ.
Author:Pelin Yilmaz
Referee:Frank Oliver Glöckner, Matthias Ullrich, Wolfgang Ludwig
Advisor:Frank Oliver Glöckner
Persistent Identifier (URN):urn:nbn:de:101:1-2013052812189
Document Type:PhD Thesis
Date of Successful Oral Defense:2011/12/09
Year of Completion:2011
Date of First Publication:2012/01/25
PhD Degree:Bioinformatics
School:SES School of Engineering and Science
Other Organisations Involved:Max-Planck-Institut für Marine Mikrobiologie (marmic)
International Max Planck Research School of Marine Microbiology (MarMic)
Library of Congress Classification:Q Science / QH Natural history - Biology / QH301-705.5 Biology (General) / QH324 Methods of research. Technique. Experimental biology / QH324.2 Data processing. Bioinformatics
Call No:Thesis 2011/48

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