This short pencast is for introduces the algorithm for global sequence alignments used in bioinformatics to facilitate active learning in the classroom.
Пікірлер: 91
@megandamico78954 жыл бұрын
This was potentially the best explanation of global alignment I've had. Thank you so much for being an awesome communicator!
@GrumpyCoder9 ай бұрын
Finally what I was searching for. Best explanation after watching many videos. Thank you!!
@sublimetrance5 жыл бұрын
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.
@sublimetrance5 жыл бұрын
Oh and THANK YOU for posting this!!! Our professor tried to explain this and did not explain it as cogently as you did!!!!
@fatemehkamalvand44623 жыл бұрын
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.
@alliedaniel57223 жыл бұрын
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!!!
@Omeruy2 жыл бұрын
Ma'm you just saved my life. It was almost like my lecturer and you were explaining two completely different things. Thank you
@guanyubi71464 жыл бұрын
This is the best and clearest explanation that I've ever see for global alignment! Great thanks!
@fed39193 жыл бұрын
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.
@danleach42174 жыл бұрын
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!
@Vincent6Liu4 жыл бұрын
Best explanation on global sequence alignment I found on the internet
@xinhaoshao42444 жыл бұрын
the best video about sequence alignments I've watched so far
@mik06113 жыл бұрын
had this in class yesterday and was utterly confused, but I definitely got it now. thank you so much!
@aylinonay41233 жыл бұрын
I cant thank you enough. I literally understood this concept with your video. You are the best!
@Jgt00213 жыл бұрын
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
@lorenlaunen34384 жыл бұрын
This is a really outstanding explanation. I'm going to assign it to my class. Thank you.
@yukipeng74293 жыл бұрын
why in the right corner you picked gap -3 instead of mismatch -2? -2 is a smaller number than -3
@Mc.Gucket6 ай бұрын
Did u find the answer
@voxlz4 жыл бұрын
Great video, you made me realize that you don't always add the cost, but alternate between cost and gap!
@shanemoe90985 жыл бұрын
You really explained this clearly in a short amount time. Very good and impressive. Kudos to you
@firebraingames3 жыл бұрын
Thank you so much! You explained better than most university professors
@yossinahmias90213 жыл бұрын
This is by far the best explanation !
@bnpqowl3 жыл бұрын
Fantastic video! Your explainations helped me to connect so many concepts. This was extremely helpful!
@owenjones67845 жыл бұрын
Deborah you are a Godsend this video was EXACTLY what I needed I love you
@tomatotree3 жыл бұрын
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?
@cynddiabalamurugan6929 Жыл бұрын
Yeah it should be -2 right?
@surviving774 жыл бұрын
Thank you! I will definitely share this with my class and cite your video.
@matthewbillman44855 жыл бұрын
2:24 "And then MATH happens!" Actually though, this helped a lot - thank you!
@brucekang64744 жыл бұрын
Thank you for your kindly explanation. you just enlightened me.
@Evkamat4 жыл бұрын
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?
@maelc92064 жыл бұрын
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!
@tecfy0284 жыл бұрын
@@maelc9206 saved my life with this explanation! *-*) hard to hear and understand every bit when English creates a barrier...
@maelc92064 жыл бұрын
@@tecfy028 I'm french so I'm glad that I understood everything, and that you understood my explanation too !
@dickspookysspookyvideos21609 ай бұрын
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 :)
@austinbvi4 жыл бұрын
Incredible explanation, thank you Deborah!
@CROXoDyLE2 жыл бұрын
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.
@Hamza-pw2yz4 жыл бұрын
this the best explanation i had seen for this algorithms thank you so much that's help me a lot
@mint-ef2up2 жыл бұрын
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!!!
@onursimsek60944 жыл бұрын
This is exactly what I want.Thank you very much
@ulma58835 жыл бұрын
Great - thank you so much for this explanation!
@yamenajjour11513 ай бұрын
great explanation !
@damlacorut22275 жыл бұрын
Thank you, that was really helpful. Hope you continue doing more videos :)
@nguyenhuythai15 Жыл бұрын
This video helps me a lots. Thank you so much 💙
@duraidmaihoub61962 жыл бұрын
Thank you for this awesome explanation ❤
@abdullahsheriff_ Жыл бұрын
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.
@ZuzanaHerciková-w7b5 күн бұрын
Thank you very much ❤ u helped me a lot 😊
@umartemiraliev6561 Жыл бұрын
thanks you very much miss! It really helped
@bishwadeepsikder30184 жыл бұрын
Thank you so very much.. The best explanation ever
@aidanakaripbayeva86344 жыл бұрын
Thank you so much, everything was clear!
@calmroad5 жыл бұрын
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.
@goheekyong89485 жыл бұрын
This was very helpful. Thanks a lot Deborah!
@natashasalmelin7205 жыл бұрын
Awesome video! Thank you!
@weiyingwang25335 жыл бұрын
Thank you! Your video is clear and helpful!
@bichngoccaotran11094 жыл бұрын
Very clear, thank you !
@subashchandrapakhrin35374 жыл бұрын
Thank you ... Great explanation.
@agustinottolini44935 жыл бұрын
Very helpful video, thank you so much!
@giorgiobarigelletti34193 жыл бұрын
Thanks! It helped me a lot!
@harishpenumati76132 жыл бұрын
Can you make a video on space efficient sequence alignment problem as well or share any of your resources regarding that
@henriquefeitosa80274 жыл бұрын
very good explanation, thanks so much :)
@dongmonguimfackmich7752 Жыл бұрын
Best video I've watched so far on this topic, Thank you!
@MagmaNeos1124 жыл бұрын
Thank you so much for your explanation! It helps me a lot:D
@tianwang84112 жыл бұрын
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.
@largelad19832 жыл бұрын
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
@zhennie73123 жыл бұрын
Thank you!!!
@Mr.Opinion3 жыл бұрын
great explanation
@annakh95433 жыл бұрын
very good explanation
@savashzaynal65022 жыл бұрын
This is great explanation but how did you even back track the path that part was not clear to me?
@gargimahajan22734 жыл бұрын
Thank you! Video was really helpful)
@RogerLuo19954 жыл бұрын
Very good!
@apologetics-1017 ай бұрын
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!
@kiranthota51373 жыл бұрын
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.
@zhennie73123 жыл бұрын
Needleman is the last name of one of the men who created this algorithm
@MLDawn5 жыл бұрын
I wonder how machine learning could be used here! (If it could)
@augustofranco1665 жыл бұрын
Thank you, good video.
@AhmedAlharbi_13 жыл бұрын
Thank you شكراً
@gloriachoi36634 жыл бұрын
THANK YOU!!!
@filmypromotionclips55842 жыл бұрын
Thank you
@PImmaluffelum4 жыл бұрын
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
@alexanderhearn6015Ай бұрын
what if a mismatch value is not given?
@dARKf3n1Xx4 жыл бұрын
Best.
@wu15092 жыл бұрын
if question doesn't give the value of match how can i know that
@amirhosseinsaemi91384 жыл бұрын
you saved my life babe!
@waliullah70514 жыл бұрын
well define mam but didnt understand the score inthe square
@BigRedVan4 жыл бұрын
Great video, feel free to take a breath though haha
@davebusch15713 жыл бұрын
she sounds a little bit nervous :-D but good video thanks for that
@stinkygaming4204 жыл бұрын
thanks
@fury1kid5 жыл бұрын
👊🏾
@nicholaswomack90274 жыл бұрын
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
@Supreme-fl8oz4 жыл бұрын
Gang shit
@mavisdracula9704 жыл бұрын
You're breathing to the microphone
@henrihauspy21273 жыл бұрын
try to breath enough :) you sound like you are out of breath all the time :) otherwise the explanation for global alignment