- Видео 27
- Просмотров 200 051
Kevin Bioinformatics
Добавлен 20 май 2015
This is a channel for learning bioinformatics concepts, algorithms and data structures.
(News 28-Aug-2021: 13 new videos uploaded! Enjoy and let me know your comments!)
(News 28-Aug-2021: 13 new videos uploaded! Enjoy and let me know your comments!)
25. Three problems related to hidden Markov models
25. Three problems related to hidden Markov models
Просмотров: 921
Видео
26. The forward and backward algorithms
Просмотров 5533 года назад
26. The forward and backward algorithms
24. Markov models and hidden Markov models
Просмотров 1,6 тыс.3 года назад
24. Markov models and hidden Markov models
23. Performing text search using Burrows-Wheeler transform
Просмотров 5063 года назад
23. Performing text search using Burrows-Wheeler transform
22. Properties of Burrows-Wheeler transform
Просмотров 2593 года назад
22. Properties of Burrows-Wheeler transform
21. Suffix array and Burrows-Wheeler transform
Просмотров 1 тыс.3 года назад
21. Suffix array and Burrows-Wheeler transform
20. Demonstration of the Ukkonen’s algorithm
Просмотров 1,7 тыс.3 года назад
20. Demonstration of the Ukkonen’s algorithm
19. Constructing a suffix tree in linear time
Просмотров 5843 года назад
19. Constructing a suffix tree in linear time
18. Constructing a suffix tree in super-linear time
Просмотров 3943 года назад
18. Constructing a suffix tree in super-linear time
12. Maximum likelihood for phylogenetic tree reconstruction
Просмотров 24 тыс.7 лет назад
12. Maximum likelihood for phylogenetic tree reconstruction
10. Maximum parsimony for phylogenetic tree reconstruction (II)
Просмотров 4,1 тыс.7 лет назад
10. Maximum parsimony for phylogenetic tree reconstruction (II)
09. Maximum parsimony for phylogenetic tree reconstruction (I)
Просмотров 9 тыс.7 лет назад
09. Maximum parsimony for phylogenetic tree reconstruction (I)
08. The phylogenetic tree reconstruction problem
Просмотров 1,7 тыс.7 лет назад
08. The phylogenetic tree reconstruction problem
05. Using dynamic programming to perform global alignment - Traceback and general scoring schemes
Просмотров 17 тыс.9 лет назад
05. Using dynamic programming to perform global alignment - Traceback and general scoring schemes
06. Using dynamic programming to perform local alignment
Просмотров 4,2 тыс.9 лет назад
06. Using dynamic programming to perform local alignment
04. Using dynamic programming to perform global alignment - basics
Просмотров 5 тыс.9 лет назад
04. Using dynamic programming to perform global alignment - basics
03. Principles of dynamic programming
Просмотров 2,9 тыс.9 лет назад
03. Principles of dynamic programming
02. How difficult is sequence alignment?
Просмотров 4,7 тыс.9 лет назад
02. How difficult is sequence alignment?
Thank you so much I finally understood this one day before the final, lol
Well presented .... So Smooth !
The clarity and pace of your lectures is excellent. However, I also appreciate your attention to "smaller" details like adding captions, dividing your videos into chapters, and organizing your content into a playlist. I can imagine you put in a lot of time and work into these extra perks, and I'm really thankful you did so. Cheers from the Netherlands. :)
Thanks for your comments! Hope the videos are useful for you!
Thank you a lot!! I learned more in 10 minutes than I learned in a 3 hour class !!! Everything is clear and the slides are vet informative!!
Happy that the video was useful for you!
You explain it so well! But i wanna know if there is any reliable software recommend for sequence alignment since i found so many different software online
this is the most simplified video i have found on the internet fir alignemnts thankyou so much kevin, subscribed.
Thank you so much!
thanks a lot. that was super helpful
Very understandable and informative, thank you!
Thanks for your brilliant work!
Thanks for watching!
Wow nice explanation 🙏
Hope it was useful for you!
Well explained Sir.. Thanks for this video
Thank you for watching!
So it's basically O(2^n)?
The number of possible alignments is exponential with respect to the lengths of the input sequences, but as you can see in the later micro-modules, it is possible to find the optimal alignments in polynomial time.
Hi, why is V(a,A) = 0.7? I'm still confused on that part. Any explanation is greatly appreciated!
V(a,A) is the probability of the sub-tree rooted at node a when its parent, node d, takes nucleotide A. This probability is equal to the probability of having A at time 0 and also A at time t_{ad}=1. By the Jukes-Cantor model, this probability is 1 - 3 * alpha =1 - 3 * 0.1 = 0.7.
great and simple
Glad you liked it!
Very good videos. Thanks a lot Prof. Yip
Thanks. Hope the videos are useful for you.
雪中送炭的視頻,希望今晚都刷完
哇 講的真的好好
Thanks! Hope you enjoy the videos.
Thanks prof. Yip I am a CUHK student as well
Hi , how do you ensure that by defining likelihood as summing all the possible ancestor states will give the best parameter estimates for a particular ancestor state? I was thinking maybe different ancestor state will have different sets of best parameters.
In this approach, based on the externally specified prior distribution of the states at the root node, summing over all possible state combinations at the internal nodes gives the overall data likelihood because the different state combinations are mutually exclusive. If the basic assumptions behind this model are not true, or if additional information is available, the calculations can be modified accordingly.
Hi is this the last section of your modules ? Is it possible that I can get the slides from your modules ?
Thanks a lot for adding new videos, your videos are and very well explained.
Thanks. Hope you enjoy the videos!
wow
nice
You nailed it again Sir!
Sir, you did a really good job in this video. It's been a year since i started learning bioinformatics but I was never sure of what was going on until I came across this video. I decided to comment before even finishing the video because I already got 90 percent of the concept. Thanks a lot.
That's great. Hope you also like the other videos in this channel!
How is this calculated in bayesian terms? What are the assumed priors? This must be an infuriating probabilistic problem, if we can't even assume the distribution of mutation frequency?
the calculation of ur 2ed table is wrong
Thank you for your comment. Could you explain how it is wrong?
Thank you so much! I'm reading a publication about MSA and your videos helped me understand sequence alignment! Very wonderful explanations - by far the best video about sequence alignment on RUclips.
Thanks for watching!
I had little prior knowledge of bioinformatics, but your excellent video made me lose my fear of it, thank you so very much.
Thanks!!! this helps a lot
Thanks for watching!
Precise and well articulated. Perfect!
Thank you for watching!
this is great! Thank you so much
Thanks for watching!
This was super helpful!
Thanks for watching!
will you upload more video about bioinformatics algorithm, such as pca, umap... it's so clear for me to understand, thank you
Yes, some more videos will be uploaded in the coming months. Stay tuned!
You explained more in 11 minutes than my professor in 4 weeks, thank you
Thanks for watching!
@@KevinBioinformatics Your lectures are awesome, If any post doc position in your lab let me know
This was really helpful, and I was able to get a better understanding of this topic. Thank you!
Glad to know that! Thanks for watching.
Wow!! My name is Kevin too. So happy to subscribe to your channel🤗🤗 I really need in depth knowledge in Bioinformatics for my masters thesis.
Hope the videos are useful for you! Comments are welcome.
This is an excellent video, thank you very much!
Thank you. Hope it was useful for you.
Thanks for watching. Hope it was useful for you.
that is so clear! thank you!
Honestly, this is the best and simplest explanation
Thanks for watching. Hope it was useful for you.
excellent video - extremely concise A+ good work
Thanks for watching. Hope it was useful for you.
really helpful and easy explanation. thanks :)
Thanks for watching. Hope it was useful for you.
how do i know the distance between 2 hub is 1? where is the hint? the math also works when distance between hub go larger and the branches linking hub to B and D shorter
Sorry for the late reply -- I didn't get the email notification of your comment for some reason. That distance is 1 because it is calculated by d(AC,B)/2 + [u(AC)-u(B)]/[2(3-2)] = 6/2 + [10-14]/2 = 3 - 2 = 1.
This was very helpful. Subscribed! I look forward to watching more videos. Thank you so much.
Thanks for watching. Hope it was useful for you.
Why is it important to generate alignment sequences using protein sequences and not DNA sequences?
Usually there is a higher level of conservation at the protein level, and thus protein sequences can be better aligned than DNA sequences.
@@KevinBioinformatics thanks 😊. I have exams in two days and I really needed to understand that concept.
Very interesting explanation, Do you have the implementation in Python?
Glad that you like the explanation. I don't have an implementation in Python. I did ask students who took my course to implement the algorithm, and they have done it using different programming languages.
Here, how we calculate distance between AC and B in matrix, i don't understand
d(AC,B) = [d(A,B) + d(C,B) - d(A,C)] / 2 = [8 + 8 - 4] / 2 = 6
I really enjoy your videos! It helps me understand the concepts behind some of the programs and the methods they are using when I am doing analysis
Thanks. It is indeed important to understand the methods when using programs that implement them.