Kevin Bioinformatics
Kevin Bioinformatics
  • Видео 27
  • Просмотров 200 051

Видео

27. The Viterbi algorithm
Просмотров 1,2 тыс.3 года назад
27. The Viterbi algorithm
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
17. Suffix tree
Просмотров 5983 года назад
17. Suffix tree
16. Suffix trie
Просмотров 3573 года назад
16. Suffix trie
15. Short-read alignment
Просмотров 6243 года назад
15. Short-read alignment
14. Neighbor joining
Просмотров 27 тыс.7 лет назад
Description
13. UPGMA
Просмотров 37 тыс.7 лет назад
Description
12. Maximum likelihood for phylogenetic tree reconstruction
Просмотров 24 тыс.7 лет назад
12. Maximum likelihood for phylogenetic tree reconstruction
11. Mutation model
Просмотров 7 тыс.7 лет назад
11. Mutation model
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)
07. What are phylogenetic trees
Просмотров 1,5 тыс.7 лет назад
07. What are phylogenetic trees
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?
01. What is sequence alignment?
Просмотров 45 тыс.9 лет назад
01. What is sequence alignment?

Комментарии

  • @Maggie-xx2is
    @Maggie-xx2is 4 месяца назад

    Thank you so much I finally understood this one day before the final, lol

  • @rajaramansoundararajan8246
    @rajaramansoundararajan8246 5 месяцев назад

    Well presented .... So Smooth !

  • @allergictoalliteration6033
    @allergictoalliteration6033 9 месяцев назад

    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. :)

    • @KevinBioinformatics
      @KevinBioinformatics 9 месяцев назад

      Thanks for your comments! Hope the videos are useful for you!

  • @ndagijimanafrankaimeerodri8893

    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!!

  • @alexlee3511
    @alexlee3511 Год назад

    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

  • @preetyyadav8543
    @preetyyadav8543 Год назад

    this is the most simplified video i have found on the internet fir alignemnts thankyou so much kevin, subscribed.

  • @Angelica-dx2sr
    @Angelica-dx2sr Год назад

    Thank you so much!

  • @Nokoli_
    @Nokoli_ Год назад

    thanks a lot. that was super helpful

  • @lotuzz7409
    @lotuzz7409 Год назад

    Very understandable and informative, thank you!

  • @pccfs
    @pccfs 2 года назад

    Thanks for your brilliant work!

  • @chitranshsinghchauhan6338
    @chitranshsinghchauhan6338 2 года назад

    Wow nice explanation 🙏

  • @sbdranjani
    @sbdranjani 2 года назад

    Well explained Sir.. Thanks for this video

  • @dariusduesentrieb
    @dariusduesentrieb 2 года назад

    So it's basically O(2^n)?

    • @KevinBioinformatics
      @KevinBioinformatics 2 года назад

      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.

  • @lyhongngoc4038
    @lyhongngoc4038 2 года назад

    Hi, why is V(a,A) = 0.7? I'm still confused on that part. Any explanation is greatly appreciated!

    • @KevinBioinformatics
      @KevinBioinformatics 2 года назад

      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.

  • @mohamedkafafy6832
    @mohamedkafafy6832 2 года назад

    great and simple

  • @oldPrince22
    @oldPrince22 2 года назад

    Very good videos. Thanks a lot Prof. Yip

  • @oldPrince22
    @oldPrince22 2 года назад

    雪中送炭的視頻,希望今晚都刷完

  • @oldPrince22
    @oldPrince22 2 года назад

    哇 講的真的好好

  • @lamjason4081
    @lamjason4081 2 года назад

    Thanks prof. Yip I am a CUHK student as well

  • @minhaoling3056
    @minhaoling3056 2 года назад

    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.

    • @KevinBioinformatics
      @KevinBioinformatics 2 года назад

      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.

  • @minhaoling3056
    @minhaoling3056 2 года назад

    Hi is this the last section of your modules ? Is it possible that I can get the slides from your modules ?

  • @AshishSingh-sy3gn
    @AshishSingh-sy3gn 2 года назад

    Thanks a lot for adding new videos, your videos are and very well explained.

  • @AdityaSharma-vi8ky
    @AdityaSharma-vi8ky 2 года назад

    wow

  • @AdityaSharma-vi8ky
    @AdityaSharma-vi8ky 2 года назад

    nice

  • @mukailarashid5428
    @mukailarashid5428 3 года назад

    You nailed it again Sir!

  • @mukailarashid5428
    @mukailarashid5428 3 года назад

    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.

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      That's great. Hope you also like the other videos in this channel!

  • @ama-tu-an-ki
    @ama-tu-an-ki 3 года назад

    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?

  • @gouthams6711
    @gouthams6711 3 года назад

    the calculation of ur 2ed table is wrong

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      Thank you for your comment. Could you explain how it is wrong?

  • @vikaanissimova6058
    @vikaanissimova6058 3 года назад

    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.

  • @MrSoumyaBanerjee
    @MrSoumyaBanerjee 3 года назад

    I had little prior knowledge of bioinformatics, but your excellent video made me lose my fear of it, thank you so very much.

  • @josephhoracek6477
    @josephhoracek6477 3 года назад

    Thanks!!! this helps a lot

  • @tayyabsheikh4021
    @tayyabsheikh4021 3 года назад

    Precise and well articulated. Perfect!

  • @asayimusa
    @asayimusa 3 года назад

    this is great! Thank you so much

  • @haleemabibi4123
    @haleemabibi4123 3 года назад

    This was super helpful!

  • @JJ-lo6up
    @JJ-lo6up 3 года назад

    will you upload more video about bioinformatics algorithm, such as pca, umap... it's so clear for me to understand, thank you

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      Yes, some more videos will be uploaded in the coming months. Stay tuned!

  • @AF-hv4yy
    @AF-hv4yy 3 года назад

    You explained more in 11 minutes than my professor in 4 weeks, thank you

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      Thanks for watching!

    • @AqleemAbbas
      @AqleemAbbas 2 года назад

      @@KevinBioinformatics Your lectures are awesome, If any post doc position in your lab let me know

  • @hannahcarrillo9435
    @hannahcarrillo9435 3 года назад

    This was really helpful, and I was able to get a better understanding of this topic. Thank you!

  • @knowledgehunter6539
    @knowledgehunter6539 3 года назад

    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.

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      Hope the videos are useful for you! Comments are welcome.

  • @oliverwilliams9507
    @oliverwilliams9507 3 года назад

    This is an excellent video, thank you very much!

  • @KevinBioinformatics
    @KevinBioinformatics 3 года назад

    Thanks for watching. Hope it was useful for you.

  • @jingzhang5008
    @jingzhang5008 3 года назад

    that is so clear! thank you!

  • @babangapu8189
    @babangapu8189 3 года назад

    Honestly, this is the best and simplest explanation

  • @gabeclark8050
    @gabeclark8050 3 года назад

    excellent video - extremely concise A+ good work

  • @inshaishrat4371
    @inshaishrat4371 3 года назад

    really helpful and easy explanation. thanks :)

  • @sumto7871
    @sumto7871 3 года назад

    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

    • @KevinBioinformatics
      @KevinBioinformatics 3 года назад

      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.

  • @sagek7949
    @sagek7949 4 года назад

    This was very helpful. Subscribed! I look forward to watching more videos. Thank you so much.

  • @arielleariella3487
    @arielleariella3487 4 года назад

    Why is it important to generate alignment sequences using protein sequences and not DNA sequences?

    • @KevinBioinformatics
      @KevinBioinformatics 4 года назад

      Usually there is a higher level of conservation at the protein level, and thus protein sequences can be better aligned than DNA sequences.

    • @arielleariella3487
      @arielleariella3487 4 года назад

      @@KevinBioinformatics thanks 😊. I have exams in two days and I really needed to understand that concept.

  • @irvingrondon3718
    @irvingrondon3718 4 года назад

    Very interesting explanation, Do you have the implementation in Python?

    • @KevinBioinformatics
      @KevinBioinformatics 4 года назад

      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.

  • @rishav513
    @rishav513 4 года назад

    Here, how we calculate distance between AC and B in matrix, i don't understand

    • @KevinBioinformatics
      @KevinBioinformatics 4 года назад

      d(AC,B) = [d(A,B) + d(C,B) - d(A,C)] / 2 = [8 + 8 - 4] / 2 = 6

  • @oglala_lakota2o
    @oglala_lakota2o 4 года назад

    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

    • @KevinBioinformatics
      @KevinBioinformatics 4 года назад

      Thanks. It is indeed important to understand the methods when using programs that implement them.