Bioinformatics Platform

The Bioinformatics Platform is build on a High Performance Computer (HPC) platform located on the ILRI campus.

Several high performance Bioinformatics packages are hosted on the HPC:

• Paracel BlastMachine (20 CPU cluster)- optimal for large BLAST searches, such as very large query sequences, or batch submission of hundreds or thousands of query sequences against a database. Implements all variants of BLAST including MegaBLAST and PSI-BLAST.
• Paracel GeneMatcher2 - extremely fast hardware acceleration of HMM, Smith-Waterman, and Genewise algorithms.
• Paracel TranscriptAssembler (PTA) software - an EST clustering and assembly package that can detect alternative splicing and chimeric transcripts.
• A growing number of publicly available software packages are also supported, and we are always open to adding whatever is needed by individual investigators.

Things you can do using the Bioinformatics Platform:

• Quickly run very large BLAST jobs on our 20-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 66 CPU Beowulf Linux cluster, or use it as a compute farm for serial jobs.
• Sophisticated, commercial-quality EST assembly using 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.