|Query Making Options|
The informations present in MycobacRV Database can be retrieved through the "Vaccine Candidate Search" tab which takes user to the Vaccine Candidate Search query page. The information to be retrieved through this page can be divided into two layers. First Layer having general information of motif, topology, location, homology and antigenic regions and Second Layer having epitope and allergen informations for the predicted adhesins and adhesin-like proteins.
The information present in MycobacRV database can also be accessed through the "Go to Advanced Search" link.Through this page users can filter their results on the basis of Protein length, number of transmembrane spanning regions, subcellular localization, presence or absence of betawraps, paralogs, hits to Conserved Domain Database, Human Reference proteins and Prbable Adhesin Vaccine Candidate decision.(I) Query Making Through "Vaccine Candidate Search" query page
(i) Select a pathogen from the pull down menu list.
(ii) Provide an GI number corresponding to the selected pathogen. For example if user selects Mycobacterioum tuberculosis H37Rv, then the GI number provided by the user must correspond to Mycobacterioum tuberculosis H37Rv. Multiple comma separated GI numbers can also be provided eg- 57116719,57116865.
This field is optional for first layer data retrieval but must be provided to fetch second layer data. Second layer data can be retrieved corresponding to a single GI number against the pathogen selected. Click oh the Get Adhesin List to get the list of GI numbers corresponding to the selected mycobacterial species. Click this link to get the list of GI numbers corresponding to available "742 predicted adhesins and adhesin-like proteins"
|(iii) The user can also retrieve the First Layer information corresponding to a keyword. This field is optional.
|(iv) Select checkbox corresponding to the data user wants to retrieve in Data Available frame.
|(v) In the Second Layer the Conformational B-Cell Epitope data is available as flat files, these are hyper linked. The flat files can be saved by the file "save as" option by the users for future use.
(vi) Finally click the submit button. This takes users to the result page.
(vii) In the result page the entire quiried data can be saved by the user on clicking the hyperlink in blue "Export data for First Layer" which provides facility to save the First Layer Data in text file and the successive epitope and allergen hyperlinks "Export Bimas Epitope Data" etc which provides facility to save the Second Layer Data from individual servers in text files.
|(II) Query Making through MycobacRV "Advanced Search" page|
|(i) Select a pathogen from the pull down menu list.|
|(ii) Select checkbox corresponding to the data user wants to retrieve in "Show information for:" frame|
|(iii) Set the filters corresponding to the data selected through the drop down boxes.|
|(iv) Finally click the submit button which takes users to the result page.|
|(v) In the result page the entire queried data can be saved by the user on clicking the hyperlink in blue "Export" which provides facility to save the entire queried First Layer Data into a text file.|
|(III) Query Making through MycobacRV "Epitope Conservation Data" page|
|(i) Epitope Conservation Analysis was studied with respect to Mycobacterium tuberculosis H37rv strain. Click on the Get Adhesin List button to get the list of 42 GI numbers corresponding to the adhesin and adhesin like proteins of Mycobacterium tuberculosis H37rv strain.|
(ii) Provide a GI number of interest from the 42 Mycobacterioum tuberculosis H37Rv proteins. Multiple comma separated GI numbers can also be provided eg- 57116719,57116865.
(iii) Select the checkbox corresponding to the epitope prediction server of interest. Epitope conservation study is performed for all potential B cell and T Cell epitopes and further analysed for epitope conservation.
Each of the B-cell and T-cell epitope was studied whether it is conserved across all its orthologs with the help of R scripts. The epitope consevancy ratio was obtained for all the epitopes as the the (Number of Occurances of the potential epitopes accross all orthologs of the protein/Total Number of Orthologs of the Protein).. Higher the raio greater is the epitope conserved.
|(iv) After selection of the checkboxes for the desired servers, click submit to go to the results page.|
|(v) Click on "View" hyperlink from Ortholog Info to view ortholog profile and epitope information.|
|Viewing Known Vaccines Candidate Information
(i) The Mycobacterial Known Vaccine Candidate Data can be viewed by clicking the "Known Vaccines" tab.