ProtozoaDB RoadMap

Contents 1 Features being implemented now (by october 2007) 1.1 Orthologs identification 1.2 Non-redundant datasets 1.3 Similarity analyses 1.4 External ID mappings 2 Features to be implemented (by december 2007) 2.1 Search by sequence and gene ontology terms 2.2 InterPro analyses 2.3 Multiple aligments and phylogeny 3 Features for 2008 3.1 3D structures 3.2 Systems biology pipeline 4 Users suggested features 5 More data and release cycle

Features being implemented now (by october 2007)

Orthologs identification

P. falciparum, E. histolytica, T. cruzi, T. brucei and L. major (5-protozoa) using OrthoMCL

Non-redundant datasets

Cd-hit100, cd-hit90 and cd-hit 75 is being running on the whole database to obtain non-redundant datasets

Similarity analyses

BlastP with Uniref90 and RpsBlast with CDD

External ID mappings

There are no ProtozoaDB ID's, visitors can use GenBank, TcruziDB or PlasmoDB ID's to query and retrieve data from ProtozoaDB.

Features to be implemented (by december 2007)

Search by sequence and gene ontology terms

Gene Ontology and Sequence Ontology terms used to annotated 5-protozoa will loaded into ProtozoaDB, then visitors will be able to search sequences using either Gene or Sequence Ontology term.

InterPro analyses

5-protozoa will be analyzed using the most updated version of InterPro and results uploaded into ProtozoaDB

Multiple aligments and phylogeny

All 5-protozoa orthologs will be used to build multiple alignments, then phylogenetic trees will be inferred using NJ and Maximum Likelihood.

Features for 2008

3D structures

A new schema for 3D structures and druggability analyses will be developed and incorporated into ProtozoaDB

Systems biology pipeline

A preliminary/prototype pipeline to extract functional information from genomics, structural, evolutionary and expression data will be developed and implemented late 2008.

Users suggested features

ProtozoaDB will (sometime in 2008) evolve and incorporate a systems biology pipeline/workflow, so please, email us with your suggestions at: protozoadb AT biowebdb dot org

More data and release cycle

• More data (available at genbank, refseq and est) for the 5-protozoa and further protozoan species will be uploaded to ProtozoaDB as they become publicly available.

• The planned release cycle is once a year (hopefuly every fall [march-june], south hemisphere) with the possibility of more than 1 release a year, depending on the availability of data.

• Interactions with GeneDB, PlasmodB, TcruziDB, Superfamily, Uniprot and PhyloFacts are planned for 2008