MicroScope: a platform for microbial genome annotation and comparative genomics

Summary Integration of data in pathogenomics is achieved here considering three different levels of cellular complexity: (i) genome and comparative genomics, (ii) enzyme cascades and pathway analysis, (iii) networks including metabolic network analysis.After direct sequence annotation exploiting tools for protein domain annotation (e.g. AnDOM) and analysis of regulatory elements (e.g. the RNA analyzer tool) the analysis results from extensive comparative genomics are integrated for the first level, pathway alignment adds data for the pathway level, elementary mode analysis and metabolite databanks add to the third level of cellular complexity. For efficient data integration of all data the XML based platform myBSMLStudio2003 is discussed and developed here. It integrates XQuery capabilities, automatic scripting updates for sequence annotation and a JESS expert system shell for functional annotation. In the context of genome annotation platforms in place (GenDB, PEDANT) these different tools and approaches presented here allow improved functional genome annotation as well as data integration in pathogenomics.

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Microbial genomics: present and future The Third Annual Conference on Microbial Genome Sequencing, Functional Characterization and Comparative Genomics, organized by The Institute for Genomic Research (TIGR), was held in Chantilly, VA, USA, 29 January – 1 February 1999.

Trends in Microbiology ◽

10.1016/s0966-842x(99)01511-5 ◽

1999 ◽

Vol 7 (6) ◽

pp. 228-229

Author(s):

K Williams

Keyword(s):

Comparative Genomics ◽

Genome Sequencing ◽

Functional Characterization ◽

Genomic Research ◽

Microbial Genome ◽

Annual Conference ◽

Microbial Genomics ◽

The Third

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Microbial genome analysis: the COG approach

Briefings in Bioinformatics ◽

10.1093/bib/bbx117 ◽

2017 ◽

Vol 20 (4) ◽

pp. 1063-1070 ◽

Cited By ~ 27

Author(s):

Michael Y Galperin ◽

David M Kristensen ◽

Kira S Makarova ◽

Yuri I Wolf ◽

Eugene V Koonin

Keyword(s):

Genome Analysis ◽

Metabolic Pathways ◽

Genome Annotation ◽

Functional Characterization ◽

Microbial Genome ◽

Functional Categories ◽

Orthologous Genes ◽

Microbial Genomes ◽

The Past

Abstract For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.

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