DNA Sequence alignment Vll How to choose the mismatch penalty? Use theory of High Scoring Segment composition High scoring alignments will have composition qi= pp ei where q = frequency of i j pairs(target frequencies") pp - req of i, j bases in sequences being compared What would happen to the target frequencies if we doubled all of the scores? *Karlin Altschul. 1990DNA Sequence Alignment VII How to choose the mismatch penalty? Use theory of High Scoring Segment composition* High scoring alignments will have composition: qij = pi pj e λ sij where qij = frequency of i,j pairs (“target frequencies”) p , p = freq of i, j bases in sequences being compared i j What would happen to the target frequencies if we doubled all of the scores? *Karlin & Altschul, 1990