Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Bioinformatics - Genomic Computing Techniques and Applications
            

SPECIALIZED HIDDEN MARKOV MODEL DATABASES FOR MICROBIAL GENOMICS

Dept. of Biochemistry / MS200, University of Nevada at Reno, Reno, Nevada 89557, US

Hidden Markov Models (HMM's) have been proven to show greater sensitivity and selectivity when compared with a standard BLAST search. Most of the existing HMM databases, however, are trained with a wide range of data that is more general, and as such are not as specific as they could be. Indeed, many of the protein families reflect a bias towards the human data that was utilized in the training of the models. The goal of the TLFAM series of databases is to provide tools that are specific to the type of organism that you are studying. Thus, the TLAM-Pro database will be used to study prokaryotes, TLFAM-Arc is used for archaeons, and so forth. This has proven to be an advantage to those that are studying microbial genomics, but it does have some drawbacks. The limitations of the method will be discussed, as well as a simple way to get around those limitations.