HHMI News: Janelia Farm’s Newest Addition to HMMER

A few weeks after its release, the Janelia Farm’s Jackhmmer algorithm — an iterative search method in the HMMER package similar to the NCBI’s PSI-BLAST algorithm — is performing as expected.  The new algorithm takes advantage of the sophisticated probabilistic models that underpin profile Hidden Markov Models (HMMs).

Profile HMMs are the most sensitive tools to use, which is why many protein family databases use them. Bench biologists now have a fast method for discovering the likely structure of a sequence which can allow for the creation of functional hypothesis that can guide experiments.