Multiple sequence alignments allow to define informative regions of homology between sequences. Models of these regions can be constructed using some sophisticated techniques as Generalized Profiles, Hidden Markov Models (HMMs), and PSI-BLAST. These models are very effective in searching databases for distant homologous sequences and in generating accurate multiple sequence alignments.

The course introduces the profile-HMMs and PSI-BLAST technologies and their application for decyphering the modular nature of protein sequences. In addition, the course is an introduction to the MyHits environment, which has been specifically designed to facilitate the above tasks to the biologists.