Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness

Based on the experiments on 35 pairs of virus genomes using three software tools (MUMmer-3, MaxMinCluster, MSS), we show that using anchors with mismatches does increase the effectiveness of locating conserved regions ( about 10% more conserved gene regions are located, while maintaining a high sensitivity) . To generate a more comprehensive set of anchors with mismatches is not trivial for long sequences due to the time and memory limitation. We propose two practical algorithms for generating this anchor set. One aims at speeding up the process, the other aims at saving memory. Experimental results show that both algorithms are faster (6 times and 5 times, respectively) than a straightforward suffix tree based appr oach.

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