Limits...
MalVac: database of malarial vaccine candidates.

Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S - Malar. J. (2008)

Bottom Line: The results are displayed in convenient tabular format and a facility to export the entire data has been provided.The MalVac database is a "community resource".A web server MalVac for facilitation of the identification of probable vaccine candidates has been developed and can be freely accessed.

View Article: PubMed Central - HTML - PubMed

Affiliation: GN Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India. rupanjali.bhu@gmail.com

ABSTRACT

Background: The sequencing of genomes of the Plasmodium species causing malaria, offers immense opportunities to aid in the development of new therapeutics and vaccine candidates through Bioinformatics tools and resources.

Methods: The starting point of MalVac database is the collection of known vaccine candidates and a set of predicted vaccine candidates identified from the whole proteome sequences of Plasmodium species provided by PlasmoDb 5.4 release (31st October 2007). These predicted vaccine candidates are the adhesins and adhesin-like proteins from Plasmodium species, Plasmodium falciparum, Plasmodium vivax and Plasmodium yoelii. Subsequently, these protein sequences were analysed through 20 publicly available algorithms to obtain Orthologs, Paralogs, BetaWraps, TargetP, TMHMM, SignalP, CDDSearch, BLAST with Human Ref. Proteins, T-cell epitopes, B-cell epitopes, Discotopes, and allergen predictions. All of this information was collected and organized with the ORFids of the protein sequences as primary keys. This information is relevant from the view point of Reverse Vaccinology in facilitating decision making on the most probable choice for vaccine strategy.

Results: Detailed information on the patterning of the epitopes and other motifs of importance from the viewpoint of reverse vaccinology has been obtained on the most probable protein candidates for vaccine investigation from three major malarial species. Analysis data are available on 161 adhesin proteins from P. falciparum, 137 adhesin proteins from P. vivax and 34 adhesin proteins from P. yoelii. The results are displayed in convenient tabular format and a facility to export the entire data has been provided. The MalVac database is a "community resource". Users are encouraged to export data and further contribute by value addition. Value added data may be sent back to the community either through MalVac or PlasmoDB.

Conclusion: A web server MalVac for facilitation of the identification of probable vaccine candidates has been developed and can be freely accessed.

Show MeSH

Related in: MedlinePlus

The MalVac layout. All data are organized in relation to the primary key ORF ID.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2562390&req=5

Figure 1: The MalVac layout. All data are organized in relation to the primary key ORF ID.

Mentions: The ORF identification tags (ORF ID) assigned to proteins of malaria parasites as given in PlasmoDB 5.4 release of 31st October 2007 [31] were used as primary keys. The database was developed using MySQL version 4.1.20 at back end and operated in Red Hat Enterprise Linux ES release 4. The web interfaces have been developed in HTML and PHP 5.1.4, which dynamically execute the MySQL queries to fetch the stored data and is run through Apache2 server. The overall layout of MalVac is provided in Figure 1.


MalVac: database of malarial vaccine candidates.

Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S - Malar. J. (2008)

The MalVac layout. All data are organized in relation to the primary key ORF ID.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2562390&req=5

Figure 1: The MalVac layout. All data are organized in relation to the primary key ORF ID.
Mentions: The ORF identification tags (ORF ID) assigned to proteins of malaria parasites as given in PlasmoDB 5.4 release of 31st October 2007 [31] were used as primary keys. The database was developed using MySQL version 4.1.20 at back end and operated in Red Hat Enterprise Linux ES release 4. The web interfaces have been developed in HTML and PHP 5.1.4, which dynamically execute the MySQL queries to fetch the stored data and is run through Apache2 server. The overall layout of MalVac is provided in Figure 1.

Bottom Line: The results are displayed in convenient tabular format and a facility to export the entire data has been provided.The MalVac database is a "community resource".A web server MalVac for facilitation of the identification of probable vaccine candidates has been developed and can be freely accessed.

View Article: PubMed Central - HTML - PubMed

Affiliation: GN Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India. rupanjali.bhu@gmail.com

ABSTRACT

Background: The sequencing of genomes of the Plasmodium species causing malaria, offers immense opportunities to aid in the development of new therapeutics and vaccine candidates through Bioinformatics tools and resources.

Methods: The starting point of MalVac database is the collection of known vaccine candidates and a set of predicted vaccine candidates identified from the whole proteome sequences of Plasmodium species provided by PlasmoDb 5.4 release (31st October 2007). These predicted vaccine candidates are the adhesins and adhesin-like proteins from Plasmodium species, Plasmodium falciparum, Plasmodium vivax and Plasmodium yoelii. Subsequently, these protein sequences were analysed through 20 publicly available algorithms to obtain Orthologs, Paralogs, BetaWraps, TargetP, TMHMM, SignalP, CDDSearch, BLAST with Human Ref. Proteins, T-cell epitopes, B-cell epitopes, Discotopes, and allergen predictions. All of this information was collected and organized with the ORFids of the protein sequences as primary keys. This information is relevant from the view point of Reverse Vaccinology in facilitating decision making on the most probable choice for vaccine strategy.

Results: Detailed information on the patterning of the epitopes and other motifs of importance from the viewpoint of reverse vaccinology has been obtained on the most probable protein candidates for vaccine investigation from three major malarial species. Analysis data are available on 161 adhesin proteins from P. falciparum, 137 adhesin proteins from P. vivax and 34 adhesin proteins from P. yoelii. The results are displayed in convenient tabular format and a facility to export the entire data has been provided. The MalVac database is a "community resource". Users are encouraged to export data and further contribute by value addition. Value added data may be sent back to the community either through MalVac or PlasmoDB.

Conclusion: A web server MalVac for facilitation of the identification of probable vaccine candidates has been developed and can be freely accessed.

Show MeSH
Related in: MedlinePlus