Table 2

Parameter evaluation using a 454-model without flowpeak information
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

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.

Lysholm

Lysholm BMC Bioinformatics 2012 13:230   doi:10.1186/1471-2105-13-230

Open Data