Sumários

Lab #4 : Probabilistic models

27 outubro 2015, 09:30 • Ana Teresa Correia de Freitas

CpG islands identification: algorithms and Genebank annotation.

ORFinder: HMM for gene finding

Programming:
Viterbi and Forward algorithms

Lab #4 - Probabilistic models

26 outubro 2015, 14:00 • Ana Teresa Correia de Freitas

Algorithms for the identification of CpG islands

Comparison with NCBI annotation
Viterbi algorithm

Probabilistic models

26 outubro 2015, 12:30 • Ana Teresa Correia de Freitas

HMM models:

- The Evaluation problem
- The Decoding problem (Viterbi algorithm)
- Forward algorithm

Exercises - Practical course

20 outubro 2015, 17:00 • Ana Teresa Correia de Freitas

Exercise 1: Compute the shortest superstring (SHS) using the Euler algorithm

Exercise 2: Genome re-sequencing (using a BWT or Suffix tree)
Exercise 3: Search pattern with errors

Probabilistic Models

20 outubro 2015, 12:30 • Ana Teresa Correia de Freitas

Markov models

Hidden Markov models

Motivation problem: finding CpG islands