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Figure 5 | BMC Bioinformatics

Figure 5

From: MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution

Figure 5

Execution time plotted against sequence length for sequence divergence of 0.2 and 0.3, and ratio of indels of 0.225. Execution times were estimated from the average of ten simulations. (a) execution time of MCALIGN2 comparing to MCALIGN and the pair HMM method of Knudsen and Miyamoto (black points and lines for divergence of 0.2; colored points and lines for divergence of 0.3). (b) tests the correctness of the program based on execution time for sequence divergence of 0.2. All the numbers are in natural log. The slope of log(time) against log(length) is 1.91 for MCALIGN2, which means the program closely follows the expected algorithm time operation O(n2). The slope of log(time) against log(length) for PairHMM_KM is 1.78, not far away from the order n2. The pattern for MCALIGN is hard to track.

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