protein sequence

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

For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection which is time consuming and requires considerable experience.

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

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