Hidden Markov Models for biological sequence analysis: the JUCHMME package

Introduction to Hidden Markov Models (HMMs) (4 hours)

• The model

• Decoding

• Training

• Labels

Applications of HMMs (4 hours)

• The PRED-TMBB method

• Detailed examples using JUCHMME

Extensions of HMMs (4 hours)

• Methods that condition on previous observations

• Hidden Neural Networks

• Detailed examples using JUCHMME

Semisupervised methods for HMMs (4 hours):

• The self-training method

• Variants of the method

• Detailed examples using JUCHMME