9. Modeling and Discovery of Sequence Motifs

[@tempvariable]

I'm just making a list for myself it may be incomplete
12:21 Exmples of protein motifs
19:29 Ways to describe a motif
33:00 Motif finding problem
37:38 Gibbs sampling

[@sfmambero]

2:55 lecture begins

[@wimthiels638]

thanks. remark at the end regarding the shifted motifs is indeed important. without it it's hard to understand the reasoning behind bias toward G after the first iteration. (so it will also be biased towards A, but those biases are resolved to G through the shifted motif heuristic)

[@hughxiao7078]

Which category does this algorithm suite, HOMER, fall under? Enumerative, Probabilistic or Deterministic? Or maybe a collection of them all, like the WebMotifs mentioned at 1:15:14. homer.ucsd.edu/homer/introduction/basics.html

[@aref6561]

now how to do it in R or Python etc? Anyone knows?

[@jackc7069]

I'm having a bit of trouble running the code for question 1 on problem set 2 (fm-search.py). It doesn't output anything onto out.txt. Can anybody help?

[@shy9926]

24:45

[@MrTian1212]

The guy, first row, left, is eating chinses?????