Bioinformatics part 10 Local alignment (revised sequence alignment)

New revised video on Local sequence alignment with scoring matrix drawing and trace back method to draw the alignment correctly.
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[ofoegbutochukwucharles]

3 should be the correct solution since negative values are disregarded and replaced with zero in local alignment, hence it should equally be applied while performing the verification check.

So, instead of arriving at [-1 +1 +1 +1 ] = 2 it should be [0 +1 +1 +1] = 3

[Hurricane]

The ending was unbelievably awkward. You should definitely add an annotation to fix your error...

[Abhinav-kfwd]

""Gaps at the terminal region are often treated with no gap penalty"".
I read this in Jin Xiong's bioinformatics book (page no-40)

So the total score comes to be 3 which is equal to the highest value in the matrix.
Hence your cross check is correct.

Hope this solved your problem you are facing at the end part of this lecture.

[sid]

Nice video, at the end it should not be 3 and not 2 because we just aligned locally not the entire sequence, so we need not consider gap penalty.

[msm]

your earlier video was confusing, where you were only working with 1 and 0.

[snehadas]

Sir. I think the C-C box should have the value 1 since on calculating we have 2. It's positive so shouldn't 1 be placed there? Subsequently the nearby values will also change, I guess.

[vinushoby]

Before you were telling for local alignment we have to keep only 0 and 1 values
Then how comes the difference in the last box
I am totally confused
Could you explain

[manishgsrivastava]

Nice explanation but in the end no gap value will be added....max value will be +3 only (This is local alignment to get only conserved sequences without considering gap)

[saisharan]

In your earlier video you have done for negative value 0 and for positive value 1 worked with 0 and 1 whether that method is correct or not?? because I done wrong in exam by seeing that video😢

[moizgamer]

Sr end sy concept smj nae Aya, ap NY 2sry video me Bola jo largest value ho ghi wo ar end p sequence ki value same ho ghi tu hi correct ho gha, ab apny end p +3 ki bjy+2 hi kyo laghya

[swadeshibiden]

GAP score -2 or -1, please make me clear. I am confused about this GAP score.

[nitinshukla]

as here we are taking gap as 0 so A is with gap and we take 0
so 0+1+1+1 = 3
and it is correct bcz it is the highest value

[tmd]

How do I know by looking at the matrix if it is a local or global alignment?

[froycardenas]

so? what happened here eh?? it's 3 or 2 ?? so you are mistaken or what Mr? you need to revised this video and adjust it

[Mybilluji]

achhe trha se homework karke banyakar video

[mj-]

Your all the video is good bt in bioinformatics videos are not tht not correct explanation .And the ending part is so bad, u should explain that point but u end the video without clear the concept..

[rashidanoorin]

Plz solve these smith waterman local algorithm

[orlahough]

Why do you keep using sequences that align with no gaps? Stupid example.... AGAIN

[roshini]

Can you explain how to find the local alignment of followings
1- AGC
2- AAAC
Gap - -2
Match +1 and mismatch -1

[Zlappyzopstix]

This was really badly explained, try and make your vids more concise because I genuinely zoned out for 2 minutes and didn't feel like I'd missed anything important