Alignment algorithm

Question

[artist01]

Hey guys,

Recently I have been asked to implement an alignment algorithm allowing mismatch with not so much code in the script. Which is the best algorithm to implement?

Thanks for your help!

[iraun]

Hi! Is this a school/university assignment? If so, I would suggest you to start trying things and playing with the code and data a bit by yourself, without really thinking of "the best algorithm". If they are already asking you to "not write so much code", I doubt that their goal is to develop the best method to carry this task. Also, there are many and very good alignment tools out there already. I would start by taking a given sequence of length N, and extracting a subsequence from it, manually modify one letter of this subsequence and try to write code to map this subsequence into the larger sequence allowing mismatches. See this for some inspiration.

Answer 1

[M.O.L.S]

Try the Smith-Waterman (Needleman-Wunsch) algorithm.

[Jean-Karim Heriche]

Just to clarify: Smith-Waterman and Needleman-Wunsch are related but not the same algorithm. SW finds optimal local alignments, NW finds global alignments

[M.O.L.S]

The original question is Which is the best algorithm to implement?