Download help for MycobacRV Rdata

The entire data in the MycobacRV database is made available in the form of Rdata to download and analyse in R platform. In MycobacRV the First Layer having term has been given to general informations of motif, topology, location, homology and antigenic regions and Second Layer term to epitope and allergen informations for the predicted adhesins and adhesin-like proteins

The analysis can be made to obtain probable adhesin vaccine candidates (Proteins with high scoring B-cell and T cell epitopes fulling First Layer conditions) or obtaining conserved epitopes important from rational vaccine design study or other immunoinformatics studies.

All the First Layer and Second Layer data for individual species has been made together into individual Rdata. Thus there are 25 Rdata for 25 Mycobacterial strains and species. They can be downloaded together as tar-gizzped file from mycobacteria.tar.gz. It should be first unzipped and untarred by the command 'tar -xvzf mycobacteria.tar.gz'. Sample R scripts (placed in a text file named sample_scripts.txt) have been provided to fascilitate the analysis process. Each Rdata for each individual species is labelled as follows.

  • Mycobacterium abscessus ATCC 19977- mabscessus.Rdata
  • Mycobacterium avium 104- maviun104.Rdata
  • Mycobacterium avium subsp. paratuberculosis K-10- maviumparatb.Rdata
  • Mycobacterium bovis BCG str. Pasteur 1173P2- mbcgpast.Rdata
  • Mycobacterium bovis BCG str. Tokyo 172 - mbcgtok.Rdata
  • Mycobacterium bovis AF2122/97- mbovisaf.Rdata
  • Mycobacterium intracellulare ATCC 13950- mintc13950.Rdata
  • Mycobacterium leprae TN- mleprae.Rdata
  • Mycobacterium leprae Br4923- mlepraebr.Rdata
  • Mycobacterium tuberculosis 98-R604- mtb98r604.Rdata
  • Mycobacterium tuberculosis C- mtbc1.Rdata
  • Mycobacterium tuberculosis SV2- SV2.Rdata
  • Mycobacterium tuberculosis SV3- SV3.Rdata
  • Mycobacterium tuberculosis CDC1551 - mtbcdc.Rdata
  • Mycobacterium tuberculosis F11- mtbf11.Rdata
  • Mycobacterium tuberculosis H37Ra- mtbh37ra.Rdata
  • Mycobacterium tuberculosis H37Rv- mtbh37rv.Rdata
  • Mycobacterium tuberculosis Haarlem- mtbhaarlem.Rdata
  • Mycobacterium tuberculosis KZN 1435- mtbkzn1435.Rdata
  • Mycobacterium tuberculosis KZN 4207- mtbkzn4207.Rdata
  • Mycobacterium tuberculosis KZN 605- mtbkzn605.Rdata
  • Mycobacterium tuberculosis KZN R506- mtbkznR506.Rdata
  • Mycobacterium tuberculosis KZN V2475- mtbkznV2475.Rdata
  • Mycobacterium tuberculosis W-148- mtbw1481.Rdata
  • Mycobacterium ulcerans Agy99- mulcerans.Rdata

Additionally, 'mycobacrvR' package and its companion data can also be downloaded as zipped file from mycobacrvR_1.0.tar.gz and respectively. It should be first unzipped and untarred by the above mentioned command. The package 'mycobacrvR' can be installed using command 'R CMD INSTALL mycobacrvR'.

Download help for Immunoinformatics Data

Export Data option is provided against all the data fetched by the user for both first and second layers. User has to tick the checkboxes corresponding to the data interested and then press the submit button. For second layer data can be fetched agaist one or more Orf Ids(Orf ID field is compulsary for second layer). In the result page Export Data option is provided. User can export the entire data fetched by clicking on Export Data link.

Here is the list of 742 adhesin and adhesin-like proteins having extracellular and cell surface localization. Following well stuctured decision trees 426 protein sequences were obtained as most probable adhesin vaccine candidates meeting the criteria of being non-allergic, having less than two transmembrane helices, no similarity to human proteins and having high scoring B-cell and T-cell epitopes from 23 strains and species of the selected mycobacteria. A stringent criterion (S = 100, L = 1, b = T) specified in the BLASTCLUST computer program was used to identify redundancy in the set of 426 protein sequences, thereby providing a non-redundant set of 233 most probable adhesin vaccine candidates. This list of 233 non-redundant most probable adhesin vaccine candidates is available here.