This short pencast is for introduces the algorithm for global sequence alignments used in bioinformatics to facilitate active learning in the classroom.
This is the best explanation I've seen so far of the logic behind this algorithm. I watched Shomu's Biology Channel explanation of this and he just runs through through the algorithm or "rules" of how to compute the scoring matrix and do a trace back of that matrix to find the optimal alignment. Your video gives me more of an intuition of why this whole algorithm works. Kudos to you! I hate just remembering a set of rules and want to know the justification of why something like this works.
I've watched so many videos trying to understand this concept and this is the first one that actually explained it in a way I could understand without having to sit there for a half hour. I would be so lost without having watched this! Thank you so much!!!
Perfectly well explained. Was the shortest, fastest, most clear explanation of global alignment and scoring. Million thanks for your concise and clear video on this topic.
Deborah, you absolute life saver. I was left scratching my head at this topic and you have made it so abundantly clear I now feel like a fool for not understanding it in the first place!
Thanks Deborah. My professor explained the same concepts and showed us an example in 4 hours and a half and the result was that no one understood anything. Your 15 minute video cleared everything up.
at 13:39 why do we say the best thing to do is to match CC instead of mismatch C and T? You go from -2 to -3 instead of going from -2 to -2 which is maximal.
Great explanation, I just have 1 question: At 14:11 why is the gap on the horizontal sequence ( the vertical line) happens between the (-1) and (-3) on column 3 R to L? I’m confused because the gap can also happen between the last T and C (or vertical line between -2 and -2 on col 2 R to L) as well right?
thanks, you made good explanations how to calculate following to the algorithm. but if you know, let me know why the gap is used. the straitforward effect of the gap shows the step expansion of the string. and the other question is, how we understand this algorithm should find best matched string.
I have a question about the scoring, Do we say the score for the sequence at the end of your video is '-1' (i.e.) the score of the cell where we start tracing back, or do we say it's '+1', since there's a '+1' along the way. In simple words, are we considering the scores of the sub-sequences while scoring the sequence? P.S. I have a gut feeling we don't consider the scores of the sub-sequences, so the answer's '-1'. Tell me what you think.
I get it till the last path. Why it goes through the -3, not diagonal to -2 and then down to -2. Didn't check if the matrix is correctly filled, but shouldn't the path go through the highest score?
If I understand correctly, you don't want to start from the top left and follow the highest score way. As she said at 13:27, you start from the bottom right, and you go up to the "number" that you originaly came from. We start at -1, we came from -2 because we did (-2 +1 = -1), so we go to that -2. Then, we went to that -2 by doing (-3 + 1 = -2). So we go to that -3. And it is infact the highest way in the end : not on the graph, because it is just a representation, but in the final alignment. Her (correct) solution gave : -1. Your solution gives : ACGGCT-C ATGGCCTC 1 -3 +1 +1 +1 -3 -4 +1 = -5 Hope I helped!
Thanks for the explanation! I have a question regarding the path, when starting from the bottom right corner (-1), it came from -2, then -3. So, my question is could this -3 come from -4 as well (on diagonal as C-C is a match, (-4) + 1 = -3)? Then 0, and the rest keeps the same. In that case, besides the alignment result on the video, another possible alignment is ACGG-CTC to ATGGCCTC.
Late answer- but potentially useful to new people with the same question. The path follows the way that you got to the maximum score, while -2 is greater than -3 that is only because the path is calculated assuming it goes from -3 to -2. If you went from -2 to -2, the matrix value would be -6, as you are adding a gap value to -2 which makes the total value for that path -8 making it suboptimal. The values on the matrix are optimal only if you follow a certain path
This was a really good video, but I have two questions: 1) In BLAST, it tries to find a local alignment, but, as I understand it, LASTZ is a global alignment, & in BLAST you can set for only the "best hit" but in a global alignment is this necessary? 2) Would you grant me permission to use timestamp: 08:39-14:26 to be used in an upcoming video on my channel? Thank you!
Thank you so much. I have one doubt, the example which we discussed are we using "Needleman-Wunsch algorithm" in here. i'm bit confused with words, Dynamic programming and Needleman. Could you please leave a comment on this.
Guys I got a large project I've been procrastinating on due tomorrow and I don't know what I'm doing. I'm in over my head I'm freaking terrified I need to graduate this semester
This was potentially the best explanation of global alignment I've had. Thank you so much for being an awesome communicator!
This is the best explanation I've seen so far of the logic behind this algorithm. I watched Shomu's Biology Channel explanation of this and he just runs through through the algorithm or "rules" of how to compute the scoring matrix and do a trace back of that matrix to find the optimal alignment.
Your video gives me more of an intuition of why this whole algorithm works. Kudos to you! I hate just remembering a set of rules and want to know the justification of why something like this works.
Oh and THANK YOU for posting this!!! Our professor tried to explain this and did not explain it as cogently as you did!!!!
I've watched so many videos trying to understand this concept and this is the first one that actually explained it in a way I could understand without having to sit there for a half hour. I would be so lost without having watched this! Thank you so much!!!
Perfectly well explained. Was the shortest, fastest, most clear explanation of global alignment and scoring. Million thanks for your concise and clear video on this topic.
Finally what I was searching for. Best explanation after watching many videos. Thank you!!
Deborah, you absolute life saver. I was left scratching my head at this topic and you have made it so abundantly clear I now feel like a fool for not understanding it in the first place!
This is the best and clearest explanation that I've ever see for global alignment! Great thanks!
had this in class yesterday and was utterly confused, but I definitely got it now. thank you so much!
Thanks Deborah. My professor explained the same concepts and showed us an example in 4 hours and a half and the result was that no one understood anything. Your 15 minute video cleared everything up.
You really explained this clearly in a short amount time. Very good and impressive. Kudos to you
Ma'm you just saved my life. It was almost like my lecturer and you were explaining two completely different things. Thank you
thank you! I never really got the hang of dynamic programming in school, but this is clear enough that I get it now! you're a great teacher :)
I cant thank you enough. I literally understood this concept with your video. You are the best!
the best video about sequence alignments I've watched so far
This is a really outstanding explanation. I'm going to assign it to my class. Thank you.
Deborah you are a Godsend this video was EXACTLY what I needed I love you
Best explanation on global sequence alignment I found on the internet
Great - thank you so much for this explanation!
Fantastic video! Your explainations helped me to connect so many concepts. This was extremely helpful!
Incredible explanation, thank you Deborah!
why in the right corner you picked gap -3 instead of mismatch -2? -2 is a smaller number than -3
Did u find the answer
Thank you! I will definitely share this with my class and cite your video.
Best video I've watched so far on this topic, Thank you!
This was very helpful. Thanks a lot Deborah!
Great video, you made me realize that you don't always add the cost, but alternate between cost and gap!
Thank you for your kindly explanation. you just enlightened me.
Thank you! Your video is clear and helpful!
This is by far the best explanation !
at 13:39 why do we say the best thing to do is to match CC instead of mismatch C and T? You go from -2 to -3 instead of going from -2 to -2 which is maximal.
This is exactly what I want.Thank you very much
this the best explanation i had seen for this algorithms thank you so much that's help me a lot
Thank you, that was really helpful. Hope you continue doing more videos :)
Thank you so much, everything was clear!
Awesome video! Thank you!
Very helpful video, thank you so much!
Thank you so much for your explanation! It helps me a lot:D
Thank you so much! You explained better than most university professors
This video helps me a lots. Thank you so much 💙
Thank you so very much.. The best explanation ever
Great explanation, I just have 1 question:
At 14:11 why is the gap on the horizontal sequence ( the vertical line) happens between the (-1) and (-3) on column 3 R to L?
I’m confused because the gap can also happen between the last T and C (or vertical line between -2 and -2 on col 2 R to L) as well right?
Yeah it should be -2 right?
Very clear, thank you !
Thank you for this awesome explanation ❤
Thank you ... Great explanation.
great explanation !
thanks, you made good explanations how to calculate following to the algorithm. but if you know, let me know why the gap is used. the straitforward effect of the gap shows the step expansion of the string. and the other question is, how we understand this algorithm should find best matched string.
2:24 "And then MATH happens!"
Actually though, this helped a lot - thank you!
Thanks! It helped me a lot!
I'm an MSc student who has reviewed this concept a few times and this is by far the best explanation I have found, thank you so much
I have a question about the scoring,
Do we say the score for the sequence at the end of your video is '-1' (i.e.) the score of the cell where we start tracing back, or do we say it's '+1', since there's a '+1' along the way.
In simple words, are we considering the scores of the sub-sequences while scoring the sequence?
P.S.
I have a gut feeling we don't consider the scores of the sub-sequences, so the answer's '-1'. Tell me what you think.
very good explanation, thanks so much :)
thanks you very much miss! It really helped
Thank you!!!
Thank you! Video was really helpful)
I get it till the last path. Why it goes through the -3, not diagonal to -2 and then down to -2. Didn't check if the matrix is correctly filled, but shouldn't the path go through the highest score?
If I understand correctly, you don't want to start from the top left and follow the highest score way.
As she said at 13:27, you start from the bottom right, and you go up to the "number" that you originaly came from. We start at -1, we came from -2 because we did (-2 +1 = -1), so we go to that -2.
Then, we went to that -2 by doing (-3 + 1 = -2). So we go to that -3. And it is infact the highest way in the end : not on the graph, because it is just a representation, but in the final alignment.
Her (correct) solution gave : -1.
Your solution gives :
ACGGCT-C
ATGGCCTC
1 -3 +1 +1 +1 -3 -4 +1 = -5
Hope I helped!
@@maelc9206 saved my life with this explanation! *-*)
hard to hear and understand every bit when English creates a barrier...
@@tecfy028 I'm french so I'm glad that I understood everything, and that you understood my explanation too !
Thank you, good video.
THANK YOU!!!
Thank you
شكراً
Thank you
great explanation
very good explanation
Can you make a video on space efficient sequence alignment problem as well or share any of your resources regarding that
oh my god, why am I paying my university when I could be paying you instead... Thank you so much for the glass-clear explanation!!!
Very good!
Thank you for the great explanation. Can you please make a Video on global alignment with affine gap penaltys? I cant figure it out :D
I wonder how machine learning could be used here! (If it could)
thanks
Thanks for the explanation! I have a question regarding the path, when starting from the bottom right corner (-1), it came from -2, then -3. So, my question is could this -3 come from -4 as well (on diagonal as C-C is a match, (-4) + 1 = -3)? Then 0, and the rest keeps the same. In that case, besides the alignment result on the video, another possible alignment is ACGG-CTC to ATGGCCTC.
Late answer- but potentially useful to new people with the same question.
The path follows the way that you got to the maximum score, while -2 is greater than -3 that is only because the path is calculated assuming it goes from -3 to -2.
If you went from -2 to -2, the matrix value would be -6, as you are adding a gap value to -2 which makes the total value for that path -8 making it suboptimal.
The values on the matrix are optimal only if you follow a certain path
This was a really good video, but I have two questions: 1) In BLAST, it tries to find a local alignment, but, as I understand it, LASTZ is a global alignment, & in BLAST you can set for only the "best hit" but in a global alignment is this necessary? 2) Would you grant me permission to use timestamp: 08:39-14:26 to be used in an upcoming video on my channel? Thank you!
Best.
This is great explanation but how did you even back track the path that part was not clear to me?
👊🏾
Thank you so much. I have one doubt, the example which we discussed are we using "Needleman-Wunsch algorithm" in here. i'm bit confused with words, Dynamic programming and Needleman. Could you please leave a comment on this.
Needleman is the last name of one of the men who created this algorithm
if question doesn't give the value of match how can i know that
Great video, feel free to take a breath though haha
well define mam but didnt understand the score inthe square
you saved my life babe!
she sounds a little bit nervous :-D but good video thanks for that
Gang shit
Guys I got a large project I've been procrastinating on due tomorrow and I don't know what I'm doing. I'm in over my head I'm freaking terrified I need to graduate this semester
You're breathing to the microphone
try to breath enough :) you sound like you are out of breath all the time :) otherwise the explanation for global alignment