This is a repository of the tools written at the Monash Proteomics Facility

• best_seqid: searches through a list of protein seqid's and looks up uniprot to find the longest and best-reviewed seqid's.

• cluster_peptides: a tool to cluster overlapping peptides together, and identify a kernel of shortest motifs

• cluster_protein_sets: for a given set of peptide-protein matches, groups together peptides that are found in the same protein

• coverage_overlay: this takes a series of peptides in the ProteinPilot 4 summary form and combines them together into one large file where a table shows in which file that a peptide was detected.

• down_pilot: a simple conversion tool for ProteinPilot 5 down to ProteinPilot 4

• format_uniprot: for the TPP package, fasta files need to be preprocessed to change the name entries. Although a perl script is provided, this does it in python.

• tpp: python module to run some TPP tools