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Design and Development of a Database for the Classification of Corynebacterium glutamicum Genes, Proteins, Mutants and Experimental Protocols
University of Skövde, School of Humanities and Informatics.
2006 (English)Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Coryneform bacteria are largely distributed in nature and are rod like, aerobic soil bacteria capable of growing on a variety of sugars and organic acids. Corynebacterium glutamicum is a nonpathogenic species of Coryneform bacteria used for industrial production of amino acids. There are three main publicly available genome annotations, Cg, Cgl and NCgl for C. glutamicum. All these three annotations have different numbers of protein coding genes and varying numbers of overlaps of similar genes. The original data is only available in text files. In this format of genome data, it was not easy to search and compare the data among different annotations and it was impossible to make an extensive multidimensional customized formal search against different protein parameters. Comparison of all genome annotations for construction deletion, over-expression mutants, graphical representation of genome information, such as gene locations, neighboring genes, orientation (direct or complementary strand), overlapping genes, gene lengths, graphical output for structure function relation by comparison of predicted trans-membrane domains (TMD) and functional protein domains protein motifs was not possible when data is inconsistent and redundant on various publicly available biological database servers. There was therefore a need for a system of managing the data for mutants and experimental setups. In spite of the fact that the genome sequence is known, until now no databank providing such a complete set of information has been available. We solved these problems by developing a standalone relational database software application covering data processing, protein-DNA sequence extraction and

management of lab data. The result of the study is an application named, CORYNEBASE, which is a software that meets our aims and objectives.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2006. , 24 p.
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:his:diva-23OAI: oai:DiVA.org:his-23DiVA: diva2:2584
Presentation
(English)
Uppsok
Physics, Chemistry, Mathematics
Supervisors
Examiners
Available from: 2006-11-06 Created: 2006-11-06 Last updated: 2009-12-02

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Bioinformatics (Computational Biology)

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CiteExportLink to record
Permanent link

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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf