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Table 1 Parameter evaluation using a non-454 model

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

Parameters/ID 40% 50% 60% 70% 80% 90% 100%
S = 10, D = 20, F = 0 0.1098 0.1064 0.1259 0.2216 0.2566 0.3099 0.3512
S = 8, D = 14, F = 0 0.1006 0.1092 0.1310 0.2332 0.2659 0.3245 0.3632
S = 8, D = 12, F = 0 0.0976 0.1074 0.1333 0.2323 0.2672 0.3232 0.3619
S = 6, D = 10, F = 0 0.0703 0.0834 0.1087 0.2350 0.2613 0.3292 0.3684
S = 6, D = 12, F = 0 0.0731 0.0909 0.1122 0.2346 0.2635 0.3317 0.3707
S = 8, D = 15, F = 0 0.1012 0.1070 0.1311 0.2332 0.2664 0.3251 0.3638
  1. The table describes the Matthews Correlation Coefficient of the homopolymer insertion/deletion recovery for various gap costs using a non-454 data model. The results are evaluated using alignments against database entries of a protein identity ranging from 40 to 100%, not including potential sequencing errors. The best results are highlighted in bold for each column. The parameter set which results in the best mean MCC is highlighted in bold.