EMBRACE

ConsensusPathDB is a database that integrates pathway and interaction resources like Reactome, HumanCyc, IntAct, Pathway Interaction Database and others. ConsensusPathDB contains biochemical reactions, protein interactions, genetic interactions, gene regulatory interactions and drug-target interactions involving different types of physical entities like genes, RNA, proteins, complexes, metabolites. The provided web services offer pathway analysis functionality for user-specified lists of genes or metabolites. For detailed information, please read:

mprap predicts the relative surface accessibility of a protein sequence. The predictor is optimized for membrane proteins.

WHAT-IF Web Services, see http://swift.cmbi.ru.nl/whatif and http://wiws.cmbi.ru.nl/help for more information.

engineDB is a repository for precalculated functional analogouse gene products using the gene ontology (GO) annotation to calculate the functional analogy by semantic similarity.

The GO data used are from the GO database version 08_09.

engineDB_08_09 is a web service accessing the engineDB searching for two gene groducts (UniProt primary accession number) the functional similarity indicating the coresponding raw score and p-value (see http://funcnet.eu)

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

• a file containing the sequences to analyse in fasta format