Create DnaAlignment.py

Author: Jinglin-LI

DnaAlignment.py

@@ -0,0 +1,67 @@
+'''
+DNA Alignment
+Needleman-Wunsch Exercise
+
+1. Two random sequences must be provided to the students.
+2. A standard scoring system needs to be shown to the students. Example: +2 for a match, -1 for a mismatch, -2 for a gap.
+'''
+
+def sequenceAlign(seqA, seqB):
+
+    DNA = {'G': { 'G':2, 'C':-1, 'A':-1, 'T':-1 },
+           'C': { 'G':-1, 'C':2, 'A':-1, 'T':-1 },
+           'A': { 'G':-1, 'C':-1, 'A':2, 'T':-1 },
+           'T': { 'G':-1, 'C':-1, 'A':-1, 'T':2 }}
+    
+    numI = len(seqA) + 1
+    numJ = len(seqB) + 1
+    scoreMatrix = [[0] * numJ for x in range(numI)]             # Initiate scoreMatrix and routeMatrix, all 0
+    routeMatrix = [[0] * numJ for x in range(numI)]
+
+    for i in range(1, numI):
+        for j in range(1, numJ):
+            gapPenalty = -2                                     # -2 for gap
+            similarity = DNA[seqA[i - 1]][seqB[j - 1]]          # +2 for match, -1 for dismatch
+            paths = [scoreMatrix[i - 1][j - 1] + similarity,
+                     scoreMatrix[i - 1][j] + gapPenalty,
+                     scoreMatrix[i][j - 1] + gapPenalty]
+            best = max(paths)
+            route = paths.index(best)
+            scoreMatrix[i][j] = best
+            routeMatrix[i][j] = route
+
+    alignA = []
+    alignB = []
+    i = len(seqA)
+    j = len(seqB)
+    score = scoreMatrix[i][j]                                   # store the score in the scoreMatrix[i][j]
+
+    while i > 0 or j > 0:                                       # Traceback
+        route = routeMatrix[i][j]
+        if route == 0:                                          # that score comes from diagonal
+            alignA.append(seqA[i - 1])
+            alignB.append(seqB[j - 1])
+            i -= 1
+            j -= 1
+        if route == 1:                                          # that score comes from vertical, gap in seqB
+            alignA.append(seqA[i - 1])
+            alignB.append('-')
+            i -= 1
+        if route == 2:                                          # that score comes from horizon, gap in seqA
+            alignA.append('-')
+            alignB.append(seqB[j - 1])
+            j -= 1
+    alignA.reverse()
+    alignB.reverse()
+    alignA = ''.join(alignA)
+    alignB = ''.join(alignB)
+
+    return score, alignA, alignB
+
+score, alignA, alignB = sequenceAlign('GGCTCAATCA', 'ACCTAAGG')
+
+print(score)
+print(alignA)
+print(alignB)
+        
+