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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.