MalVac: Database of Malarial Vaccine Candidates (Version 1.1)
Rupanjali Chaudhuri, Institute of Genomics and Integrative Biology
18 May 2010
Authors:Srinivasan Ramachandran , Ab Rauf Shah and Rupanjali Chaudhuri*
Address: G.N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
Email: Ab Rauf Shah – abraufshah@gmail.com; Rupanjali Chaudhuri* - rupanjali.bhu@gmail.com; Srinivasan Ramachandran - ramuigib@gmail.com * Corresponding author
Abstract We have updated the MalVac database to MalVac version1.1. The set of predicted vaccine candidates from the whole proteome provided by the most recent PlasmoDB 6.3 release(12 March 2010) has been incorporated into the updated MalVac database. The predicted vaccine candidates are adhesin and adhesin like proteins from the malaria causing Plasmodium species, P.falciparum, P.vivax and P.yoelii and subsequenly analysed with immunoinformatics algorithms. The new version is freely available at http://malvac.igib.res.in.
Letters to the Editor
Dear Professor Marcel Hommel,
MalVac: Database of malarial vaccine candidates[1] was developed with a set of predicted adhesin vaccine candidates from the protein sequences of three Plasmodium species, Plasmodium falciparum, Plasmodium vivax and Plasmodium yoelii taken from PlasmoDB 5.4 release(31st October 2007). The updated protein sequences were retrieved from PlasmoDB version 6.3[2]. These sequences were analyzed as described previously [1] and MalVac was updated to MalVac version 1.1 available as a malaria community resource.
Updation Process Protein sequences from the three Plasmodium species were run through MAAP, a malaria adhesin and adhesin like proteins predictor[3]. Protein sequences predicted to be malarial adhesins emerged as 163 protein sequences from P. falciparum, 139 protein sequences from P. vivax and 34 protein sequences from P. yoelii. The ORF ids of the sequences were compared to those of our previous list compiled from a MAAP run on Plasmodb 5.4 release. Among the entries with same ORF Id a BlastP run was carried out to examine for any sequence changes in the new release.
All newly added predicted vaccine candidates along with the ones whose sequences had been updated by PlasmoDB 6.3 were analysed through 20 algorithms important from view of reverse vaccinology as described previously [1]. Some of these algorithms used for collecting analytical data housed in our previous version of MalVac have now updated to new versions. These are NetMHC 3.0[4] used for the prediction of T cell epitopes, Conserved Domain Database and Search Service, v2.20[5] used to predict conserved domains and Discotope 2.0[6] used to predict conformational B cell epitopes. Hence all the predicted vaccine candidates- 163 from P. falciparum, 139 from P. vivax and 34 from P. yoelii were re-analysed through the updated algorithms. All data emerging from the new analysis were compiled into MySQL Database. The rest 17 algorithms were unchanged.
On comparison of the present version with the previous one, the updation consisted of removal of 7,and 4, protein sequences each from P. falciparum and P. vivax. None of the protein sequences removed were experimentally known plasmodium adhesins. On the other hand 9 new protein sequences from P. falciparum and 6 new protein sequences from P.vivax were predicted as adhesins in the MAAP run with new release. Most these new proteins are hypothetical proteins. In P. falciparum two exported proteins (PHISTa like) and a MORN repeat protein are included. In P. vivax a variable surface protein- Vir 18 is included. The Vir 18 protein is proposed to be involved in host pathogen interaction[7]. There was no change in the list of predicted adhesin proteins in P. yoelii. BlastP results of sequence comparisons between same protein sequence identifiers from previous version PlasmoDB 5.4 revealed sequence updates in 6 protein sequences of P. falciparum and 1 protein sequence of of P. vivax. The blast result of updated sequence comparison between 6.3 and 5.4 release of these protein sequence identifiers is summarized below: 1.PF10_0306- Differed by 1%. 2.PFE1540w-Differed by 9%. 3.PFB1055c-Differed by 2%. 4.PF10_0406-Differed by 1%. 5.PF14_0272-Differed by 22%. 6.MAL13P1.306-Differed by 3%. 7.PVX_110835-Differed by 1%. The analysis data of these newly predicted vaccine candidates along those with updated sequences have been integrated into the new MalVac version 1.1. All the query formulation features have been retained in new MalVac version1.1. The results obtained can be exported by the user in simple tab delimited text format.
Authors' contributions SR supervised the updation process. ARS and RC collected the data. RC compiled data in the MySQL database.
References 1.Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S: MalVac: Database of malarial vaccine candidates.Malar J. 2008, 7:184. 2.Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H.PlasmoDB: a functional genomic database for malaria parasites.Nucleic Acids Res. 2009, 37(Database issue):D539-43. Epub 2008 Oct 28. 3.Ansari FA, Kumar N, Bala Subramanyam M, Gnanamani M, Ramachandran S: MAAP: Malarial adhesins and adhesin-like proteins predictor.Proteins 2008, 70:659-666. 4.Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S: Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 2003, 62:378-384. 5.Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly.Nucleic Acids Res. 2004 .32(Web Server issue):W327-31. 6.Andersen P H, Nielsen M, Lund O: Prediction of residues in discontinuous B cell epitopes using protein 3D structures. Protein Science 2006, 15:2558-2567. 7.Janssen CS, Phillips RS, Turner CM, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucleic Acids Res 2004;32:5712–5720.
Competing interests
The authors declare that they have no competing interests.
MalVac: Database of Malarial Vaccine Candidates (Version 1.1)
18 May 2010
Authors:Srinivasan Ramachandran , Ab Rauf Shah and Rupanjali Chaudhuri*
Address: G.N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
Email: Ab Rauf Shah – abraufshah@gmail.com; Rupanjali Chaudhuri* - rupanjali.bhu@gmail.com; Srinivasan Ramachandran - ramuigib@gmail.com
* Corresponding author
Abstract
We have updated the MalVac database to MalVac version1.1. The set of predicted vaccine candidates from the whole proteome provided by the most recent PlasmoDB 6.3 release(12 March 2010) has been incorporated into the updated MalVac database. The predicted vaccine candidates are adhesin and adhesin like proteins from the malaria causing Plasmodium species, P.falciparum, P.vivax and P.yoelii and subsequenly analysed with immunoinformatics algorithms. The new version is freely available at http://malvac.igib.res.in.
Letters to the Editor
Dear Professor Marcel Hommel,
MalVac: Database of malarial vaccine candidates[1] was developed with a set of predicted adhesin vaccine candidates from the protein sequences of three Plasmodium species, Plasmodium falciparum, Plasmodium vivax and Plasmodium yoelii taken from PlasmoDB 5.4 release(31st October 2007). The updated protein sequences were retrieved from PlasmoDB version 6.3[2]. These sequences were analyzed as described previously [1] and MalVac was updated to MalVac version 1.1 available as a malaria community resource.
Updation Process
Protein sequences from the three Plasmodium species were run through MAAP, a malaria adhesin and adhesin like proteins predictor[3]. Protein sequences predicted to be malarial adhesins emerged as 163 protein sequences from P. falciparum, 139 protein sequences from P. vivax and 34 protein sequences from P. yoelii. The ORF ids of the sequences were compared to those of our previous list compiled from a MAAP run on Plasmodb 5.4 release. Among the entries with same ORF Id a BlastP run was carried out to examine for any sequence changes in the new release.
All newly added predicted vaccine candidates along with the ones whose sequences had been updated by PlasmoDB 6.3 were analysed through 20 algorithms important from view of reverse vaccinology as described previously [1]. Some of these algorithms used for collecting analytical data housed in our previous version of MalVac have now updated to new versions. These are NetMHC 3.0[4] used for the prediction of T cell epitopes, Conserved Domain Database and Search Service, v2.20[5] used to predict conserved domains and Discotope 2.0[6] used to predict conformational B cell epitopes. Hence all the predicted vaccine candidates- 163 from P. falciparum, 139 from P. vivax and 34 from P. yoelii were re-analysed through the updated algorithms. All data emerging from the new analysis were compiled into MySQL Database. The rest 17 algorithms were unchanged.
On comparison of the present version with the previous one, the updation consisted of removal of 7,and 4, protein sequences each from P. falciparum and P. vivax. None of the protein sequences removed were experimentally known plasmodium adhesins. On the other hand 9 new protein sequences from P. falciparum and 6 new protein sequences from P.vivax were predicted as adhesins in the MAAP run with new release. Most these new proteins are hypothetical proteins. In P. falciparum two exported proteins (PHISTa like) and a MORN repeat protein are included. In P. vivax a variable surface protein- Vir 18 is included. The Vir 18 protein is proposed to be involved in host pathogen interaction[7]. There was no change in the list of predicted adhesin proteins in P. yoelii.
BlastP results of sequence comparisons between same protein sequence identifiers from previous version PlasmoDB 5.4 revealed sequence updates in 6 protein sequences of P. falciparum and 1 protein sequence of of P. vivax. The blast result of updated sequence comparison between 6.3 and 5.4 release of these protein sequence identifiers is summarized below:
1.PF10_0306- Differed by 1%.
2.PFE1540w-Differed by 9%.
3.PFB1055c-Differed by 2%.
4.PF10_0406-Differed by 1%.
5.PF14_0272-Differed by 22%.
6.MAL13P1.306-Differed by 3%.
7.PVX_110835-Differed by 1%.
The analysis data of these newly predicted vaccine candidates along those with updated sequences have been integrated into the new MalVac version 1.1. All the query formulation features have been retained in new MalVac version1.1. The results obtained can be exported by the user in simple tab delimited text format.
Authors' contributions
SR supervised the updation process. ARS and RC collected the data. RC compiled data in the MySQL database.
References
1.Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S: MalVac: Database of malarial vaccine candidates.Malar J. 2008, 7:184.
2.Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H.PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009, 37(Database issue):D539-43. Epub 2008 Oct 28.
3.Ansari FA, Kumar N, Bala Subramanyam M, Gnanamani M, Ramachandran S: MAAP: Malarial adhesins and adhesin-like proteins predictor. Proteins 2008, 70:659-666.
4.Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S: Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 2003, 62:378-384.
5.Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 .32(Web Server issue):W327-31.
6.Andersen P H, Nielsen M, Lund O: Prediction of residues in discontinuous B cell epitopes using protein 3D structures. Protein Science 2006, 15:2558-2567.
7.Janssen CS, Phillips RS, Turner CM, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucleic Acids Res 2004;32:5712–5720.
Competing interests
The authors declare that they have no competing interests.