INRIA-UCBL

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

ProdomCG_evoscen is a set of webservices allowing to browse ProDom-CG267 evolutionary scenarios. It includes

• GetScenarioProdom : takes an ProDom-CG family (CG + 6 characters) and returns its evolutionary scenario as a string of (number of nodes) characters (absence = 1, presence = 2)
• GetPresentFamiliesProdom : takes a taxID present in ProdomCG and returns a list of ProdomCG families present at this node

ProdomCG_tree is a set of webservices allowing to browse ProDom-CG267 phylogenetic tree. It includes

• NearestNodeProdom : takes an NCBI taxID and returns the closest taxID present in ProdomCG
• GetParentProdom : takes a taxID present in ProdomCG and returns its parent
• GetChildProdom : takes a taxID present in ProdomCG and returns its child(ren)
• GetDFStreeProdom : returns the list of all the taxIDs present in ProdomCG in DFS order

Hogenom_evoscen is a set of webservices allowing to browse Hogenom 4 evolutionary scenarios. It includes

• GetScenarioHogenom : takes an Hogenom family (HBG + 6 digits) and returns its evolutionary scenario as a string of (number of nodes) characters (absence = 1, presence = 2)
• GetPresentFamiliesHogenom : takes a taxID present in Hogenom and returns a list of Hogenom families present at this node
• GetInheritedFamiliesHogenom : takes a taxID present in Hogenom and returns a list of Hogenom families inherited at this node

Hogenom_tree is a set of webservices allowing to browse Hogenom 4 phylogenetic tree. It includes

• NearestNodeHogenom : takes an NCBI taxID and returns the closest taxID present in Hogenom
• GetParentHogenom : takes a taxID present in Hogenom and returns its parent
• GetChildHogenom : takes a taxID present in Hogenom and returns its child(ren)
• GetDFStreeHogenom : returns the list of all the taxIDs present in Hogenom in DFS order