Table 2

Effect of match reward and mismatch penalty on specificity and sensitivity of contiguous and discontiguous MegaBLAST searches

% total BESs

% BESs positioned

Parameters


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

77.57%

31.91%

41.14%

2

-3

Discontiguous2

54.92%

21.94%

39.95%

1

-1

51.17%

22.64%

44.24%

2

-3


1word size 11, with no score filtering

2word size of 11 with a match length of 21 using a discontiguous seed, with no score filtering

Ratnakumar et al. BMC Genomics 2010 11:458   doi:10.1186/1471-2164-11-458

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