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Bioinformatics Shared Resources
Sanford Burnham Prebys Medical Discovery Institute
About the BSR
Services & Pricing
Systems & Data
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
how to load it)
- a desktop DNA sequence viewer and annotation tool (PC and Mac).
Package for DNA sequence preprocessing, assembly and editing.
is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
is a desktop program for primer design and analysis (PC and Mac).
Creates dot-plot similarity matrix between DNA-DNA, protein-protein and DNA-protein sequences
A suite of programs for searching DNA/protein sequence databases
Multiple sequence alignment program for both protein and DNA.
Estimate phyolgenetic relationships using Bayesian statistics.
Java tool for the visualization of annotated phylogenetic trees.
3D Molecular Structure
Visually sophisticated tool for creating publication or presentation quality 3D images of molecular structures.
Simple but powerful desktop structure visualization and annotation tool. Runs on PC, Mac, Unix.
Microarray and Gene Expression
Electron density map improvement
Phasing program for multiple wavelenth data sets
Structure determination suite
Automated structure determination from MIR, SAD or MAD data
x-ray detector sofware for monochromatic data
provides facilities for conversion and processing of 1D-4D NMR spectra
A program for the visualization and analysis of NMR datasets