Articles

• Implementing Gotoh

  Nov 5, 2016

  In the previous two posts (1, 2), I introduced sequence alignments for affine gap cost functions and an efficient algorithm to compute them. Here I would like to discuss how to implement it efficiently.

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• The algorithm of Gotoh

  Nov 4, 2016

  In the last article, I introduced the sequence alignment problem. What I did not tell you is that it is practically useless for any real-world application. Oops, I am sorry about that!

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• Sequence alignment

  Nov 3, 2016

  Sequence alignment arguably is one of the classic and fundamental problems in bioinformatics. It is not just that it has obvious applications (homology modelling, gene finding, evolutionary distances, …) and not so obvious applications, but the efficient algorithms for it (e.g. Needleman-Wunsch, Smith-Waterman, Gotoh, just to mention the most prominent ones) follow an algorithmic paradigm that can be applied to solve various optimization problems (to be precise, the ones following Richard Bellman’s Principle of Optimality). On top of that, one can learn a great deal about programming when implementing these algorithms.

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