CMBspr06Asn3 - Assignment 3(points 50 Due March 2 06(1...

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Assignment 3 (points 50, Due: March 2, 06) (1) Implement the global alignment dynamic programming algorithm. Input: two strings, and a scoring scheme. Output: the global score, the aligned sequences, and some measure of performance. (Submissions: hard copy, and demo. Comments should indicate your name, the algorithm, any other discussions, etc.) Test: dfuoiuhfdshfkflkfldsfhhfdshfalkhffhsdjkfhsd dfdoiuffdshfflkfldscdhdshfalkhffhsdjkertd Result: dfd oiuf fdshf-flkfldscd h-dshfalkhffhsdjkert d (2) Modify the program to handle semi-global alignment. Test: dshfkflkfldsfhhfdshfalkhffhsdjkfhsd dfuoiuhfdshfkflkfldkfhhfdshfalkhffhsdjk Result: --------dshfkflkfldsfhhfdshfalkhffhsdjkfhsd dfuoiuhfdshfkflkfldk fhhfdshfalkhffhsdjk---- (3) Modify the program to handle local alignments above an input threshold. Test: dfuoiuhfdshfkflkfldsfhhfdshfalkhffhsdjkfhsd qwhfsdkffhsdjyiyiufdshtyfkflkiop Result: dfuoiuhfdshfkflk fldsfhhfdshfalkhffhsd jkfhsd qwhf sd k-ffhsd jyiyiufdsh ty fkflk iop (4) A small string <i>t</i> has to be searched within a larger string <i>s</i> with usual alignment algorithm. Obviously you do expect lots
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