ok...here's the function I've written so far. def padWithGaps(seq): for letter in seq: letter="-" line=len(seq) dashline=line*letter return dashline def replace(someString,position,letter): first=someString[0:position] second=letter third=someString[position+1:len(someString)] newString=first+second+third return newString ##findScore("MPFVS","MS-V-") would return a score of 2 def findScore(first,second): count=0 for position in range(0,len(first)): if first[position]==second[position]: count=count+1 position=position+1 return count #shorter is a 3 amino acid sequence ##longer is any length sequence greater than 3 ###i=first amino acid; j=second amino acid; k=third amino acid def findAlignment(shorter,longer): for i in range(0,len(longer)-2): for j in range(1,len(longer)-1): for k in range(2,len(longer)): dashline=padWithGaps(longer) nextLine=replace(dashline,i,shorter[0]) nextNext=replace(nextLine,j,shorter[1]) alignment=replace(nextNext,k,shorter[2]) score=findScore(longer,alignment) ####don't know what to do here print longer print alignment print "Score = " + str(score) I don't know what to do at the end of my loop but what I'm trying to do in pseudocode is: "if that alignment has the best score seen so far save the score and the alignment print the best score and the best alignment"
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