This is the code repository for the multiple search engine framework, developed at the Universities of Manchester and Liverpool, in the groups of Simon Hubbard and Andy Jones.

The core algorithm is described in:

Jones AR, Siepen JA, Hubbard SJ, Paton NW. Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics. 2009 9(5):1220-9. http://www3.interscience.wiley.com/journal/122221188/abstract

The code calculates FDR, based on decoy database searching, for each search engine and assigns a FDR Score to every identification.

The web-based implementation is hosted here: http://www.ispider.manchester.ac.uk/FDRAnalysis/FDR_analysis_home.html

A desktop implementation is available to Windows users as a beta version by following these steps:

1. Install Java, version 6 or later.
2. Install Perl, version 5.8 or later.
3. Go to 'Downloads' and download FDRApp.zip.
4. Unzip FDRApp.zip. This will create a new directory called 'FDRApp', containing a file called RunDesktopApp.bat.
5. Run RunDesktopApp.bat by double-clicking it.

To report bugs or request help with the Desktop application only, please contact Paul Blackhurst: pblackATliv.ac.uk (replace AT with @)