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Figure 4 | Algorithms for Molecular Biology

Figure 4

From: Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences

Figure 4

"Slope zone" of the Smith-Waterman global alignment and density of reference and random alignments. A, B - evolutional distance of 30PAM; C, D - evolutional distance of 120PAM. A, C - console length r = 100%; B, D - console length r = 200%. Mean densities of reference (D glob ) and random (D rand ) alignments and mean accuracy of Smith-Waterman global alignments (Glb.Accur) versus the asymmetry value of consoles c at evolutional distances 30 and 120PAM and consoles of 100% and 200% length of the core length of the sequences. The intersection of straight lines - plots of the D glob and D rand values corresponds to the beginning of the "slope zone" of the accuracy plot (see also Fig. 3). Densities of Smith-Waterman global alignments are given for comparison. Here the intersection of plots for D glob and D rand values is typically close to the point where the plot for D sw passes the zero value. At rather high c values the density of algorithmic global alignments (D sw ) is close to the density of random alignments (D rand ).

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Algorithms for Molecular Biology

ISSN: 1748-7188