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299
Appendix B
APPENDIX B
Nucleotide Scoring Schemes
Nucleotide scoring schemes are often summarized by their target frequency, which is
the expected frequency of nucleotide pairs. This frequency is usually expressed as the
expected percent identity. For example, the +1/-1 match/mismatch values have a tar-
get frequency of 75 percent identity. But this is true only for ungapped alignments
between sequences of infinite length. Short sequences and gapped alignment change
the true target frequency. In the following table, the target frequencies for a variety of
match (+), mismatch (-), and simple gap costs (gap) are calculated for pairs of
sequences of length 100, 500, and 1,000 by performing local alignments of random
nucleotide sequences of unbiased composition. The theoretical target frequency (TF)
is included for comparison.
+ - Gap TF 100 500 1,000
11175554949
11275797069
11375857979
12295938988
12395989696
12495989797
13399999998
54465514848
54565534949
54665555049
54765595150
54865625250
54965645553
5 4 1065675957
5 4 1165696160
5 4 1265716362
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Appendix B: Nucleotide Scoring Schemes
55575554949
55675595150
55775645553
55875706159
55975726564
5 5 1075797069
5 5 1175807371
5 5 1275817574
5 5 1375827676
5 5 1475827777
5 5 1575857979
56682625351
56782696058
56882756765
56982797371
5 6 1082837775
5 6 1182857979
5 6 1282878181
5 6 1582908584
5 6 1882908786
57787736463
57887787270
57987837776
5 7 1087878281
5 7 1187898483
5 7 1287908685
5 7 1387918887
5 7 1487918887
5 7 2187939190
58890817573
58990858079
5 8 1090898584
5 8 1190918786
5 8 1290928988
5 8 1390939089
5 8 1490939190
5 8 1590949291
+ - Gap TF 100 500 1,000
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Nucleotide Scoring Schemes
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301
5 8 1690949392
5 8 2490959493
59993868281
5 9 1093908685
5 9 1193928989
5 9 1293939190
5 9 1393939291
5 9 1493949291
5 9 1593959392
5 9 1693959493
5 9 1793959493
5 9 1893959494
5 9 2793969594
5 101095938988
5 101195949290
5 101295959391
5 101395959493
5 101495959496
5 101595989696
5 102095989797
5 103095989897
+ - Gap TF 100 500 1,000
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