Needleman Wunsch Algorithm|| Dynamic Programming|| Bioinformatics|| Part # 02 (Example)

[@amanjaved3095]

This video really helped to understand how to fill in the table. Thank you so much

[@edobajoyce]

Whoaa! Eureka!! it wasn't so hard after listening to every explanation. Merci!!

[@BioScholar971]

You're welcome! I'm glad the explanation helped. If you have any more questions or need further assistance, feel free to ask.

[@mynameisminhhoang]

Thank you so much, it helps me pass the test. Wish you the best

[@BioScholar971]

You're very welcome! I'm so glad I could help you pass the test. Thanks for sharing your experience. Your feedback is highly appreciated.

[@victorpeng5355]

sure is tricky but definitely helped! thank you

[@Akam_J_Mustafa]

Well done 👏, this video really helped me to understand NW algorithm matrix. Thanks

[@BioScholar971]

Glad it helped!

[@adamoadam6244]

Isn't T A - T G A T A C - G A with gaps, so the best alignment would be TACTGA ?

[@DimitriTrubetskoy]

Great. thanks as well. Now it is clear. Though, you could explain it even a little bit more, with some shifting square for example, and explaining where each number is coming from every time. Even if you said that technically, it's not obvious from the first approach. Thanks anyways

[@BioScholar971]

You're welcome! Thank you for sharing your feedback. I appreciate your suggestions and will keep them in mind for future explanations.

[@erikOHsix06]

so what is the possible alignment at the end? I can't see it because the "Bio Scholar" logo is in the way

[@BioScholar971]

T A T G A T A C G A

[@santiagovega6870]

hello! I understand that negative values ​​are placed directly as 0, so the first row and the first column are all 0

[@BioScholar971]

In the Smith-Waterman algorithm, the matrix is initialized with zeros on both sides. However, in the Needleman algorithm, the matrix is initialized by progressively incorporating gap penalties from the start. If you have any other question feel free to ask.

[@justem_things7016]

sir i think the value for 5th column and 2nd row is wrong ie., for G and T respectively. please have a look and if not please clear by doubt

[@BioScholar971]

(For G and T) Incorporate gap penalties when assessing the top and left values: Top value: (−8)+(−2)=−10 Left value: (−3)+(−2)=−5 Add the mismatch penalty when considering the diagonal value: Diagonal value: (−6)+(−1)=−7 From these computed values (-10, -5, and -7), select the highest, which is -5.

[@anandsagar1351]

thankyou .. by mistake i was also doing the wrong and having same doubt now it is clear.

[@justsmile2me]

I'm curious if the opening gap penalty and extension gap penalty is different.

[@BioScholar971]

Yes, the opening gap penalty and extension gap penalty are typically different. The opening gap penalty is the penalty incurred for starting a gap in the alignment, while the extension gap penalty is the penalty incurred for continuing an existing gap. If the alignment algorithm is aligning two sequences that are very similar and there are no significant insertions or deletions. In this case, the algorithm may choose to use the same gap penalty for both opening and extending gaps in order to favor more aligned positions.

[@UCSRAHULMAURYA]

does match and mismatch scores are pre decided as 1 and -1 or it can be changed?....can match score be assumed as +5 and mismatch as -1??

[@ramizj.m5675]

All of the scoring systems of sequence alignment are arbitrary, except for those which aim to assess the biological properties of the sequences for a possible substitution of an amino acid with another one. So theoretically yes you can change those reward/penalty points as long as you use the same values for all the alignment scores.

[@Nandhini-s2m]

3rd row and 3rd c and t how to 1 please explain that

[@BioScholar971]

Check description, Pdf link is mentioned.

[@nitehok600]

what would be the alignment score and how do you find it?

[@BioScholar971]

For match score is (1) and for mismatch score is (-1). So, the overall score for the alignment is 3. T A C G A T A T G A +1 +1 (-1) +1 +1 +4 -1 =3

[@BioScholar971]

If you have any other question feel free to ask.

[@nitehok600]

@@BioScholar971 For the second sequence above, you mean 'G' not 'C' right?

[@BioScholar971]

Yes, its G not C

[@nitehok600]

@@BioScholar971 In what case would there be a dash in the alignment?

[@nitehok600]

I think the traceback path you took and the alignment was wrong, if you go vertical or horizontal there should be a dash on the letter you go towards. Your alignment would be (T A - T G A / T A C - G A) if you choose to go left at 1.

[@BioScholar971]

Traceback is correct, dash or hyphen is used to indicate indels.