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Open Access Highly Accessed Research article

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

Jonathan L Klassen1* and Cameron R Currie12

Author Affiliations

1 Department of Bacteriology, University of Wisconsin--Madison, Madison, Wisconsin, USA

2 DOE Great Lakes Bioenergy Research Center, University of Wisconsin--Madison, Madison, Wisconsin, USA

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BMC Genomics 2012, 13:14  doi:10.1186/1471-2164-13-14

Published: 10 January 2012

Additional files

Additional file 1:

Parameterization of the fragment linkage algorithm by varying the maximum percentage identities, sequence overlap and minimum difference in the percent identities of a set protein fragments to a complete reference homolog. False and true positive linkage results were defined based on their concordance with the adjacent location of each fragment pair on the same contig. Each analysis was conducted on the entire Streptomyces test dataset except for Streptomyces sp. PP-C42, for which there was not available scaffold information.

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Additional file 2:

Parameterization of the fragment linkage algorithm by varying the maximum percentage of identities and sequence overlap while holding the minimum difference in the percent identities of a set protein fragments to a complete reference homolog constant at 40%. The height of the surface represents the number of fragments matched using each parameter combination, and the color represents the percentage of true positives recovered using those parameters by reference to the available scaffold information.

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Open Data