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Nucleic Acids Research, 2003, Vol. 31, No. 17 e106
© 2003 Oxford University Press

MGView: an alignment and visualization tool to enhance gap closure of microbial genomes

Lisa Herron-Olson, John Freeman1, Qing Zhang, Ernest F. Retzel1 and Vivek Kapur*

Departments of Microbiology and Veterinary Pathobiology and Biomedical Genomics Center, University of Minnesota, St Paul, MN 55108, USA and 1 Center for Computational Genomics and Bioinformatics, University of Minnesota, Minneapolis, MN 55455, USA

*To whom correspondence should be addressed at 1971 Commonwealth Avenue, St Paul, MN 55108, USA. Tel: +1 612 625 7712; Fax: +1 612 625 5203; Email: vkapur{at}umn.edu

Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conservation of genetic information between microbial genomes, combined with the exponential increase in available microbial sequences, can be exploited to increase the efficiency of gap closure, we lack the computational tools to aid in this process. We describe here a new tool, MGView, which was developed to create a graphical depiction of the alignment of a set of microbial contigs against a completed microbial genome. The results of our assembly of the Staphylococcus aureus RF122 genome show that MGView enables a considerable reduction in time and economic cost associated with closure. Together, the results also show that the application of MGView not only enables a reduction in fold-coverage requirements of the random shotgun sequence phase, but also provides interesting insights into differences in gene content and organization between finished and unfinished microbial genomes.


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