Sequence Alignment | Needleman Wunsch Algorithm

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Explanation step by step of how the sequence alignment algorithms problem works. Other common names of this algorithm is the Needleman Wunsch algorithm. In the next video we will code this algorithm from scratch using Python. On Leetcode this algorithm can be found under "Edit Distance", it seems this algorithm has many different names!
Code Repository:
github.com/Ala...

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21 окт 2024

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Комментарии : 22

@maocafez2948 2 года назад

This is the most clear tutorial for sequence alignment I have ever seen!!! Thank you sooo much!!! Finally I understand the inner principle instead of just computing according to the formula :)

@bweasles1 4 года назад

Hey thank you so much for the video! it was very clear. Just one question - while backtracking (~17:15), you state that deleting the G, aligning the C and adding the A to the end is the best option, even though just aligning G to C and C to A has the same cost. How do you differentiate between those two to pick a best transformation?

@AladdinPersson 4 года назад

I think when there are two ways of achieving the same lowest cost, you just pick one of them. In the python code for sequence alignment if several would be equal I just (arbitrarily) chose insert, then align and lastly delete (code: github.com/aladdinpersson/Algorithms-Collection-Python/blob/5109ccaf3ec09031d7e1f135e3492d8180026b43/Algorithms/dynamic_programming/sequence_alignment.py#L45-L55)

@maocafez2948 2 года назад

I have the same question before. I think that's because you want to do sequence aligning, so you do not want mismatch, so you will choose the insert or delete way.

@alirezaghaffartehrani1279 2 года назад

Thanks for making this video to further understanding of this algorithm. However I did not find the link to the Python coding! Is it not yet prepared?

@dannyisrael 3 года назад

Thanks! What school did you go to? Seems to be clearly from the kleinberg and tardos textbook. Very useful!

@MatheusAugustoGames 4 года назад

Amazing video. The ending felt a bit rushed, but the explanation is still understandable. I wonder if this algorithm is applicable in logic languages (e.g, Prolog).

@AladdinPersson 4 года назад

I appreciate the kind words🙏

@fahadrazzaq711 3 года назад

Is it for optimal global alignment or maximal global alignment? What's the difference in implementing both?

@petrosstyle2981 4 года назад

the last 1 minute of the video needs more explanation, it is the critical alignment part.

@AladdinPersson 4 года назад

What did you feel was missing from the explanation?

@LearnWithAbubakr 2 года назад

well explained except the last section (how to find the solution).

@irvingrondon3718 4 года назад

Do you have a video, implementing this Alignment Explained | Needleman Wunsch in Python?

@AladdinPersson 4 года назад

Yes, here: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-XmyxiSc3LKg.html

@irvingrondon3718 4 года назад

@@AladdinPersson I am following your python code!. Very nice, clear, and useful video. Do you have more python codes in Bioinformatics? Thank you very much!

@AladdinPersson 4 года назад

@@irvingrondon3718 No I haven't done much algorithms at all, my more recent videos are towards machine learning and deeplearning, but might do more of these in the future. What video topics do you think would be interesting?

@irvingrondon3718 4 года назад

Do you have the Needleman-Wunsch algorithm implentation in the matrix representation as en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm