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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute


Software resources available at SanfordBurnham. Some of the software is maintained by IT on a server while other titles can be downloaded and used directly from your computer.

Below is a list of software organized by category: 

Systems biology software and toold

  • We use: Ingenuity IPA, MetaCore (Thomson Reuters), NextBio, GeneSpring, TRANSFAC and Oncomine. 

Statistical analysis software

  • We use: R, Partek, SAS and Excel data analysis toolpak
  • Available for use by other researchers at SBMRI: GraphPad Prizm (contact IT for install help) and Excel data analysis toolpak (see here how to load it)


  • Artemis - a desktop DNA sequence viewer and annotation tool (PC and Mac).
  • Staden Package Package for DNA sequence preprocessing, assembly and editing.
  • RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  • Oligo is a desktop program for primer design and analysis (PC and Mac).


  • Dotter  Creates dot-plot similarity matrix between DNA-DNA, protein-protein and DNA-protein sequences
  • Blast  A suite of programs for searching DNA/protein sequence databases


  • T-Coffee Multiple sequence alignment program for both protein and DNA.


  • MrBayes Estimate phyolgenetic relationships using Bayesian statistics.
  • ATV Java tool for the visualization of annotated phylogenetic trees.

3D Molecular Structure

  • PyMol Visually sophisticated tool for creating publication or presentation quality 3D images of molecular structures.
  • RasMol Simple but powerful desktop structure visualization and annotation tool.  Runs on PC, Mac, Unix.

Microarray and Gene Expression

  • GeneSpring
  • BioConductor
  • GenePattern


  • GenePattern
  • Mascot
  • Trans-Proteomic Pipeline


  • ccp4
  • CNSsolve
  • HKL
  • O
  • Resolve Electron density map improvement
  • SHARP/autoSHARP Phasing program for multiple wavelenth data sets
  • Shelx97 Structure determination suite
  • Solve Automated structure determination from MIR, SAD or MAD data
  • XDS x-ray detector sofware for monochromatic data


  • NMRpipe provides facilities for conversion and processing of 1D-4D NMR spectra
  • NMRViewJ A program for the visualization and analysis of NMR datasets