• Quickly run very large BLAST jobs on our 44-CPU BlastMachine cluster.
  
  
• Search for protein domains or new genes using HMMs and Genewise on the GeneMatcher2. The GeneMatcher2 hardware tremendously accelerates HMMER, Genewise, and the Smith-Waterman algorithms.
  
  
• Look for remote homologs - run highly sensitive sequence searches using the Smith-Waterman algorithms on the GeneMatcher2 or using PSI-BLAST accelerated on the BlastMachine.
  
  
• Develop and run parallel MPI jobs on the 90 CPU Beowulf Linux cluster, or use it as a compute farm for serial jobs.
  
  
• Sophisticated, commercial-quality sequence and EST assembly using Paracel GenomeAssembler and Paracel Transcript Assembler.
  
  
• We maintain the latest copies of all major sequence databases for each of our platforms - you can set up your own pipeline to run a set of queries at regular intervals against the latest data.
  
  
• Choose from our growing list of academic software packages supported on our machines, including packages for genetic analysis and structural biology.
  
  
• Web-based and UNIX login access to the various machines. We can host large-scale projects. We are working on technologies to allow remote use of our machines.
  
  
  

Scenarios for Use of the Facility.

Example Projects