July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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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 ...
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