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Practical Innovation at BioCon 2003


The Hidden Models Revealed: a survey of HMM databases
Martin Gollery, University of Nevada, Reno

Track: Techniques
Date: Thursday, February 06
Time: 10:45am - 11:30am
Location: California Ballroom C

Hidden Markov Models (HMMs) provide a wealth of information that can be used to mine EST and genomic data in a tremendously effective way. Many HMM programs have been available for years, both in the accelerated and non-accelerated forms. Gollery examines all of these implementations, but the real emphasis in this talk will be the HMM databases.

For years, PFAM has stood as the major HMM database in the world of bioinformatics. Curated at the Sanger center by a fine group of scientists, PFAM is a major part of the Interpro system. Gollery covers several recent improvements to the PFAM database:

  • The Superfamily database was developed by Julian Gough at the MRC in the UK. Based on the SCOP database, it can quickly identify the superfamily to which your protein of interest belongs.
  • The TIGRFAMs database is curated at The Institute for Genomic Research. The models in this database are grouped by role and subrole.
  • The SMART database (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically-mobile domains and the analysis of domain architectures.
  • The TLFAMs are a set of databases of HMMs that are trained on specific classes of organisms, and show improved sensitivity when used on new genomes of that same class.

    Download presentation file

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