Computational protocol: Community Based Case-Control Study of Rotavirus Gastroenteritis among Young Children during 2008-2010 Reveals Vast Genetic Diversity and Increased Prevalence of G9 Strains in Kolkata

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Protocol publication

[…] Nucleotide sequencing was carried out using the ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction Kit v3.1 (Applied Biosystems, Foster City, California, USA) in an ABI Prism 3730 Genetic Analyzer (PE Applied Biosystems, Foster City, California, USA) as described previously . Nucleotide and protein sequence BLAST search was performed using the National Centre for Biotechnology Information (NCBI, National Institutes of Health, Bethesda, MD) Basic Local Alignment Search Tool (BLAST) server on GenBank database release 143.0 . Pairwise sequence alignments were performed using LALIGN software (EMBnet, Swiss Institute of Bioinformatics, Switzerland), and multiple alignments were done with DDBJ software and CLUSTAL W. Amino acid sequences were deduced using the TRANSEQ software (Transeq Nucleotide to Protein Sequence Conversion Tool, EMBL-EBI, Cambridgeshire, UK). Phylogenetic tree was constructed using the MEGA (Molecular Evolutionary Genetics Analysis) program, version 6. Genetic distances were calculated using the Maximum likelihood method (500 bootstrap replicates) using the MEGA 6 program. According to model testing results, Kimura2 parameter model was selected to construct the phylogenetic dendrograms. Lineage designation for phylogenetic dendrograms of G1, G2, G9 and G12 strains were based on those reported in previous studies –. Partial nucleotide sequences of VP4 gene and complete nucleotide sequences of VP7 gene of the strains detected during this study were submitted to the GenBank database under the accession numbers: KM008633–KM008642 (G1 strains); KM008643–KM008652 (G2 strains); KM008653–KM008655 (G4 strains); KM008657–KM008666 (G9 strains); KM008667–KM008675 (G12 strains); KM008676–KM008682 (P strains); KM008683–KM008690 (P strains); KM008691–KM008699 (P strains). […]

Pipeline specifications

Software tools BLASTN, LALIGN, Clustal W, MEGA
Databases DDBJ
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Homo sapiens, Rotavirus A