Table 2 Effect of match reward and mismatch penalty on specificity and sensitivity of contiguous and discontiguous MegaBLAST searches
| Â | % total BESs | % BESs positioned | Parameters | ||
|---|---|---|---|---|---|
| Â | &positioned& | &in tail-to-tail BACs& | &in tail-to-tail BACs& | &match reward, -r& | &mismatch penalty, -q& |
Contiguous1 | 76.78% | 32.36% | 42.15% | 1 | -1 |
| Â | 77.57% | 31.91% | 41.14% | 2 | -3 |
Discontiguous2 | 54.92% | 21.94% | 39.95% | 1 | -1 |
| Â | 51.17% | 22.64% | 44.24% | 2 | -3 |