In this homework, you will implement Needleman-Wunsch algorithm and Smith-Waterm

Question

In this homework, you will implement Needleman-Wunsch algorithm and Smith-Waterman algorithm. Your program will be- given an input like the below example: First line of the input E will specify the number of symbols in the alphabet of the sequences. Second line of the input will contain E letters seperated with single space. Then E lines of input will follow, each with E numbers, which will form the similarity matrix of size E times E. Next line will contain a single number, which denotes the gap penalty. Finally last two lines present two sequences from the input alphabet (possibly with different lengths). You output should be as in the below example: A-CACACTA AGCACAC-A First line of the output should be the similarity score of the alignment you find. Second and third lines of the output should present the alignment. All input and output will be through standart input and standart output. Please do not use any files. You might implement the algorithms on C, C++ and Java. You should follow ANSI C and ANSI C++ standarts for C and C++.

Explanation / Answer

hopefully it will help u: http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm http://www.scribd.com/doc/17601679/NeedlemanWunsch-and-SmithWaterman-Algorithm

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