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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Klassen and Currie BMC Genomics 2012 13:14 doi:10.1186/1471-2164-13-14