LecturesPart03

# And henikoff jg 1992 proc nat acad sci usa 8 9 19915

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Unformatted text preview: son of PAM250 and BLOSUM62 12 10 8 6 4 2 0 BLOSUM62 score ­2 ­4 ­6 See Demonstration A13 ­10 ­5 0 5 PAM250 score 10 15 20 Dynamic Programming Illustration with Similarity Matrix s (Demonstration A9) Extensions to basic dynamic programming alignment method s use similarity function in initialization step s allow gaps x use gap penalties use Gap penalty alternatives s constant gap penalty for gap > 1 s gap penalty proportional to gap size x one penalty for starting a gap (gap opening one penalty) penalty) x different (lower) penalty for adding to a gap different (gap extension penalty) (gap End gaps s Some programs treat end gaps as normal Some gaps and apply penalties, other programs do not apply penalties for end gaps not End gaps (cont.) x Can determine which a program does by adding Can extra (unmatched) bases to the end of one sequence and seeing if match score changes sequence x Penalties for end gaps appropriate for aligned Penalties sequences where ends "should match" sequences x Penalties for end gaps inappropriate when Penalties surrounding sequences are expected to be different (e.g., conserved exon surrounded by varying introns varying Global vs. local similarity s If doing global alignment, report traceback If for all alignments with best score for s If doing local alignment, save new trace If when the best forward path is negative and only report traceback for positive scores Formal description of NW algorithm (no gap penalties) Initialize Si,j to contain similarity scores for Initialize elements ai and bj of sequences of length m and n For i=m to 1 by -1 to For j=n to 1 by -1 For Si, j = Si, j + max{Si +1, j +1, max ( Si + x, j +1 ),max ( Si, j + y +1 )} x³ 1 y³ 1 Formal description of NW algorithm (no end gap penalties) Initialize Si,j as before Initialize as wz contains the penalty for a gap of length z>0 Now do i, j i, j i +1, j +1 S = S + max{S max (Si + x , j +1 - w x ), x³ 1 max (Si +1, j + y - w y )} y³ 1 , Formal description of full dynamic programming algorithm with end gaps (see Mount Ch. 3) s(aibj) contains similarity scores for elements ai and bj of sequences of length m and n wz contain...
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