Bioinformatics Software

The main bioinformatics software I have been involved in developing is listed below, with links to the individual websites. This software is currently undergoing reorganisation reannotation but for the time-being is packaged up under the umbrella of the Protein Evolution Analysis Toolkit (PEAT). In addition to the main programs listed, PEAT also contains a number of Accessory Applications, which have less documentation and development than the main software but may be of use to some people. Much of this software and/or the accompanying documentation is still under active development - please contact me with any questions regarding the software listed. All software is freely available under a GNU General Public License.

• Edwards RJ (2010). PICSI: Proteomics Identification from Cross-Species Inference. Cleanup of Proteomics identifications.
• Edwards RJ (2009). FIESTA: Fasta Input EST Analysis. Assembly, annotation and homology-searching EST libraries.
• Edwards RJ (2009). QSLiMFinder: Query SLiMFinder. (Novel motif discovery for a specific query.)
• Edwards RJ (2008). BUDAPEST: Bioinformatics Utility for Data Analysis of Proteomics using ESTs. Proteomics on EST data.
• Edwards RJ (2008). SLiMSearch: Short Linear Motif Search tool. (For known motifs.)
• Edwards RJ, Davey NE & Shields DC (2007). SLiMFinder: Short Linear Motif Finder. (Novel motif discovery.)
• Edwards RJ, Davey NE, Johnston CR & Shields DC (2006). SLiM Pickings: SLiMDisc results compilation and extraction.
• Edwards RJ (2006). CompariMotif: Motif-Motif Comparison Tool
• Davey NE, Shields DC & Edwards RJ (2006). SLiMDisc: Short Linear Motif Discovery. (Novel motif discovery.)
• Edwards RJ (2006). PRESTO: Protein Regular Expression Search Tool.
• Edwards RJ & Davey NE (2006). GABLAM: Global Alignment from BLAST Local Alignment Modules.
• Edwards RJ (2006). GOPHER: Generation of Orthologous Proteins from High-throughput Evolutionary Relationships
• Edwards RJ (2005). COMPASS: Comparison of Motif Predictions across Servers and Sequences.
• Edwards RJ (2005). BADASP: Burst After Duplication with Ancestral Sequence Prediction.
• Edwards RJ (2004). GASP: Gapped Ancestral Sequence Prediction.
• Edwards RJ (2002). HAQESAC: Homologue Alignment Quality, Establishment of Subfamilies and Ancestor Construction.