Pandurang Kolekar
Ph.D. Bioinformatics
Sr. Staff Bioinformatics Research Scientist
St. Jude Children's Research Hospital, Memphis, TN, USA
https://www.stjude.org/
http://orcid.org/0000-0003-0044-0076
Genotyping of Viruses
Development of genotyping server for Mumps viruses
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This project involved the development of the server for genotyping of MuV is developed and validated using SH gene sequences of known genotypes. It implements sequence-based bioinformatics approaches viz. BLAST, alignment-based Neighbor-joining phylogeny and alignment-free RTD-based approach developed in-house.
This server will be useful for epidemiological surveillance and to monitor the circulation of MuV genotypes within and across geographic areas. This will also facilitate phylodynamics studies of mumps viruses.
Team members:
Pandurang Kolekar
Dr. Mohan Kale
Dr. Urmila Kulkarni-Kale
Genotyping server for Dengue viruses
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This project involved the development of genotyping server for Dengue viruses using alignment-free RTD-based method. The server accepts complete genome sequence(s) of Dengue viruses and predicts the genotypes for the query sequences.
The performance of the server is assesed using ROC analysis with the help of true positive and true negative datasets. It was found that server has 100% sensitivity and specificity.
Kolekar et al (2012) Mol Phyl Evol, 65(2):510-522
Available at: http://bioinfo.net.in/dengue/homepage.html
Team members:
Pandurang Kolekar
Dr. Mohan Kale
Dr. Urmila Kulkarni-Kale
Kolekar et al (2014) J Virol Methods, 198: 41-55
Available at: http://bioinfo.net.in/WNV/homepage.html
Genotyping server for West Nile viruses
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Currently, genotyping of West Nile viruses (WNV) is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology.
Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. Both the method and the server have 100% sensitivity and specificity.
Team members:
Pandurang Kolekar
Nilesh Hake
Dr. Mohan Kale
Dr. Urmila Kulkarni-Kale