Highly improved homopolymer aware nucleotide-protein alignments with 454 data

BMC Bioinformatics

Table 1 Parameter evaluation using a non-454 model

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

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.

ISSN: 1471-2105