Inializaon for all i j fi 0 0 f0 j 0 2 terminaon

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: s Dan Jurafsky The Needleman ­Wunsch Algorithm •  Ini'aliza'on: D(i,0) = -i * d! D(0,j) = -j * d •  Recurrence Rela'on: D(i,j)= min D(i-1,j) - d! D(i,j-1) - d! D(i-1,j-1) + s[x(i),y(j)]! •  Termina'on: D(N,M) is distance ! ! Dan Jurafsky The Needleman ­Wunsch Matrix x1 xM y1 (Note that the origin is at the upper leB.) yN Slide adapted from Serafim Batzoglou Dan Jurafsky A variant of the basic algorithm: •  Maybe it is OK to have an unlimited # of gaps in the beginning and end: ----------CTATCACCTGACCTCCAGGCCGATGCCCCTTCCGGC GCGAGTTCATCTATCAC--GACCGC--GGTCG-------------•  If so, we don’t want to penalize gaps at the ends Slide from Serafim Batzoglou Dan Jurafsky Different types of overlaps Example: 2 overlapping“reads” from a sequencing project Example: Search for a mouse gene within a human chromosome Slide from Serafim Batzoglou Dan Jurafsky The Overlap Detec9on variant xM yN x1 Changes: 1.  Ini'aliza'on For all i, j,! !F(i, 0) = 0! !F(0, j) = 0! 2.  Termina'on ! maxi F(i, N)! y1 FOPT = max! ! maxj F(M, j)! Slide from Serafim Batzoglou Dan Jurafsky The Local Alignment Problem Given two strings x = x1……xM, y = y1……yN Find substrings x’, y’ whose similarity (op'mal global alignment value) is maximum x = aaaacccccggggXa y = Xcccgggaaccaacc Slide from Serafim Batzoglou Dan Jurafsky The Smith ­Waterman algorithm Idea: Ignore badly aligning regions Modifica'ons to Needleman ­Wunsch: Ini9aliza9on: F(0, j) = 0! ! ! !F(i, 0) = 0! 0 !! Itera9on: F(i, j) = max F(i – 1, j) – d! ! ! ! ! F(i, j – 1) – d! ! ! ! ! F(i – 1, j – 1) + s(xi, yj) Slide from Serafim Batzoglou ! Dan Jurafsky The Smith ­Waterman algorithm Termina9on: 1.  If we want the best local alignment… FOPT = maxi,j F(i, j)...
View Full Document

Ask a homework question - tutors are online