Homology The results from the preliminary analyses of homology among the 22 Protozoa are available for queries

Homology The results from the preliminary analyses of homology among the 22 Protozoa are available for queries. in Ruby language using Ruby on Rails (RoR). This new version also allows a more detailed analysis of the object of study, as well as expanding the number of genomes and proteomes available to the scientific community. In our case study, a group of prenyltransferase proteinsalready explained in the literature was found to Ospemifene be a good drug target for Trypanosomatids. Database. Open in a separate window Physique 2 The front page of ProtozoaDB 2.0 displaying database statistics, the search field, and the tags cloud. Table 1 List of organism Ospemifene species loaded in ProtozoaDB 2.0. proteome and the Conserved Domains Database. Only the top ten results are shown. Clicking on links in blue opens a new windows in the remote website. 2.3. Homology The results of the preliminary analyses of homology among the 22 Protozoa are available for questions. The orthologous groups were inferred by the methodology implemented in OrthoMCL (Physique 5) and OrthoSearch, using either a Blast-based or Hmmer-based algorithm, respectively. Open in a separate window Physique 5 Orthologous groups inferred using OrthoMCL methodology. Clicking on the Group link shows all proteins of that group that are shown in the left panel (Query Results). 2.4. Metabolic Pathways The system performs a web service-based query to retrieve metabolic maps available on KEGG, showing the involvement of a given protein PIK3R1 in that pathway (Physique 6). Open in a separate window Physique 6 Metabolic pathways from KEGG. The physique shows all metabolic pathways that include aspartate aminotrasnferase. Clicking on a map opens a new window in a remote Ospemifene web site (KEGG). 2.5. Phenotypes ProtozoaDB 2.0 allows web service-based questions through the phenotypes mapped from your Database [21], retrieving proteins from your 22 Protozoa that could potentially provide such features. This information was made possible by mapping the proteome of the 22 species with information from your KEGG orthologous groups (Kegg OrthologyKO) as part of the transformation step explained in the introduction (Physique 7). Open in a separate window Physique 7 Phenotypes found by orthology with for farnesyltransferase alpha protein subunit. 2.6. How to Search The new system retrieves the information through numerous search engines. Based on the previous version, the system searches for the description of the protein or part of the description, Accession Number, Genbank Identifier (GI), and organism name. In addition to these mechanisms, this new version also allows query by phenotype and similarity (Blast). 2.7. How to Search Using Ospemifene Our Web Service In addition we also made a set of web service functions available to retrieve all information available in our system. The page http://services.biowebdb.org/howtouse contains the information about how to use available services including Ospemifene source code examples. Functions to search Protozoa proteins by Accession Number, Genbank Identifier, description (annotation), organism, phenotype, and Blast, as well as details of protein analyses like orthologous groups, similarity results, KEGG pathways, and phenotypes, are available for queries with our web services. 2.8. Information ExtractionT. brucei Case Study To demonstrate the usefulness of ProtozoaDB 2.0 for information extraction, a case study was conducted using phenotypes in the Kinetoplastea species. Through the search field system the option Phenotypes was chosen and the keyword inviable used with the Kinetoplastea subset.