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. 2008 Apr 29;36(10):3455–3462. doi: 10.1093/nar/gkn168

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© 2008 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Performance comparison between the BLAST-end method (plotted points) and the PGA method (vertical bars) using different simulated data sets. (A) The assembly accuracies on data sets containing different numbers of simulated contigs of random fragments derived from Synechococcus sp. WH8102. The genomes of Synechococcus sp. CC9605 (S9605), Synechococcus sp. CC9902 (S9902) and P. marinus MIT 9313 (P9313) were used as the reference genomes, respectively. (B) The assembly accuracies on data sets containing different numbers of simulated contigs of random fragments derived from Shewanella sp. ANA-3. The genomes of S. oneidiensis (Sone), S. amazonensis (Sama), and S. frigidimarina (Sfri) were used as references, respectively. (C) The overall success rate for gap closure attained if one uses the four best predictions from the relaxed PGA method (PGA-extended, see text for detail) with the same data sets used in Figure 3A. (D) The overall success rate for gap closure attained using the four best predictions from the relaxed PGA method (PGA-extended, see text for detail) with the same data sets used in Figure 3B.