PeptideCutter predicts potential substrate cleavage sites, cleaved by proteases or chemicals in a given protein sequence. The tool returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions.
The Ping-Pong Algorithm (PPA) is a method for integrating tabular data sets that share a common dimension. A typical example for this is gene expression across a set of tissues and drug-response data for the same tissues. The PPA finds co-modules in the two data sets, i.e. genes that are co-expressed in some tissues that have similar responses to a subset of the drugs. The co-modules can overlap; the PPA is efficient and scales well to large data sets. A Matlab implementation is provided.
The PoPS project is a set of computational tools for investigating protease specificity. The main PoPS program allows users to model and profile protease specificity and predict substrate cleavage. Other tools are available to search for substrates within proteomes (protein databases for organisms), and create simple matrix models of specificity from experimental data.
An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to discover patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported. The patterns are reported using PROSITE syntax.
ProDom is a protein domain family database constructed automatically by clustering homologous segments. Compare your sequence with ProDom by running a Blast-P or Blast-X search against: the consensus sequence provided with the ProDom families or the multiple alignments provided with each ProDom family. ProDom-CG (Complete Genomes) and ProDom-SG (Structural Genomics Candidate Search) can also be searched.
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Scan protein sequence(s) against PROSITE, or search for hits by specific motif(s) in protein sequence database(s). ScanProsite may be used alternatively in quick scan mode or advanced scan mode.