Protein Homology Detection Through Alignment of Markov Random FieldsThis work covers sequence based protein homology detection, a fundamental and challenging bioinformatics problem with a variety of real world applications. The text first surveys a few popular homology detection methods, such as Position Specific Scoring Matrix (PSSM) and Hidden Markov Model (HMM) based methods, and then describes a novel Markov Random Fields (MRF) based method developed by the authors. MRF based methods are much more sensitive than