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Table 2 Parameter evaluation using a 454-model without 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 = 54, h = 0.2, k = 0.9, V = 1 0.415 0.415 0.462 0.493 0.538 0.571 0.605
S = 15, D = 26, h = 0.4, k = 0.6, V = 0 0.402 0.427 0.464 0.547 0.606 0.665 0.706
S = 15, D = 29, h = 0.4, k = 0.6, V = 0 0.403 0.425 0.467 0.548 0.607 0.666 0.708
S = 12, D = 24, h = 0.5, k = 0.6, V = 0 0.351 0.359 0.461 0.571 0.640 0.691 0.765
S = 8, D = 15, h = 0.7, k = 1, V = 0 0.259 0.261 0.363 0.553 0.625 0.694 0.791
  1. The table describes the Matthews Correlation Coefficient of the homopolymer insertion/deletion recovery for various parameter combinations using a 454 model without flowpeak information (i.e. FASTA 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.