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Table 3 Parameter evaluation using a 454-model using flowpeak information

From: Highly improved homopolymer aware nucleotide-protein alignments with 454 data

Parameters/ID 40% 50% 60% 70% 80% 90% 100%
S = 30, D = 60, h = 0.2, k = 0.4, V = 1 0.681 0.682 0.708 0.748 0.775 0.796 0.815
S = 30, D = 60, h = 0.2, k = 0.5, V = 1 0.681 0.683 0.712 0.752 0.782 0.803 0.823
S = 20, D = 40, h = 0.3, k = 0.4, V = 1 0.673 0.677 0.706 0.757 0.788 0.812 0.833
S = 30, D = 60, h = 0.2, k = 0.8, V = 1 0.666 0.671 0.701 0.757 0.791 0.817 0.839
S = 15, D = 30, h = 0.4, k = 0.5, V = 1 0.613 0.629 0.673 0.744 0.782 0.825 0.849
S = 8, D = 15, h = 0.7, k = 0.4, V = 0 0.321 0.317 0.455 0.639 0.697 0.774 0.862
  1. The table describes the Matthews Correlation Coefficient of the homopolymer insertion/deletion recovery for various parameter combinations using flowpeak information (i.e. SFF input). The results are evaluated using alignments against targets of a protein identity ranging from 40 to 100%, not including potential sequencing errors. The best results are highlighted in bold for each column as well as the parameter set which results in the best mean MCC (default parameters).