Improved hit criteria for DNA local alignment

BMC Bioinformatics

Table 1 Bernouilli Model Hit probability of seeds on Bernoulli sequences of length 64 with match probability 0.7 and transition/transversion probabilities 0.15

weight	spaced seed	hit proba	transition-constrained seed	hit proba
9	B₉ = ##_##_#_#___###	0.7291	B₉^tr= ##@_#@#__#_###	0.7366
10	B₁₀ = ##_##___##_#_###	0.5957	B₁₀^tr= #@#_#_@#_@#__@###	0.6056
11	B₁₁ = ###_#__#_#__##_###	0.4671	B₁₁^tr= #@#_#@__##_#_@@##	0.4784

ISSN: 1471-2105