HMM method for exploring divergent family relationships.

• A hidden Markov Matrix (HMM) is like a Psi-Blast PSSM except it also learns position specific gap penalties during training.  That means it can not only detect divergent sequences but also align them (Eddy, 1998).
• The Sequence Analysis and Modeling System (SAM) was ported to Dr. Demeler's supercomputer.
• SAM is a product of R. Hughey, A. Krogh, and K. Karplus at the UCSC computational biology center.
• SAM features context-specific prior knowledge, Dirichlet mixtures, free insertion modules, and inclusion of structural information.
• SAM was able to build a >400 member family containing all known phage (and Herpes Virus) terminase genes.
• Fig. 5;

Serwer P, Hayes SJ, Zaman S, Lieman K, Rolando M, Hardies S. 2004. Improved isolation of undersampled bacteriophages: finding of distant terminase genes. Virology, in press.
• Details of T7-like clade and immediate ancestors.
• The SAM alignment revealed structural similarities at the level of predicted 2ndary structure maps.
• Motor domain 2, endo domain, portal binding domain.
• P-loop domain.
• SAM was automated to build families for every gene in a given virus, hence making a library of family models for detecting deeply diverged family members in new phage genomes.