In-Silico Analysis of CDS for Snorkel Genes of Oryza sativa Using Bioinformatics Tools and Techniques in Deep Water Rice

Pragnya Paramita Jena; Pranati Swain; Gayatri Gouda

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Abstract
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Background: Prolonged submergence stress is a serious consequence in rice. The CDS regions of Snorkel protein were considered for the study.

Method: A brief comparative analysis has been performed by using several bioinformatics tools and techniques in order to understand the physico-chemical properties, secondary structures of conserved protein regions, multiple sequence alignment, homology models, and backbone confirmation for generated homology models.

Findings: The objective of this study was to understand the similarity among all these four CDS regions. Different bioinformatics tools PROTPARAM, CFFFSP server, CLC genomic workbench, MODELLER, RAMPAGE has been used to understand both structural and comparative differences. This insilco analysis will helpful to researchers to study more on the networking mechanism between sub1 introgressed lines and snorkel introgressed lines and mechanism involve when both the gene are introgressed together in single variety.

Application/Improvements: understanding the network mechanism in snorkel introgressed lines.