Abstract

IN SILICO APPROACH TO STUDY SEQUENCE ALIGNMENT, PREDICTION OF PRIMER AND HOMOLOGY MODELLING

Nikunj Patel, Nayan Prajapati, Richa Patel, Khushi Patel and Haresh Kalasariya*

Abstract

The aim of present study is to check the relationship between different nucleotide sequences of viruses belongs to Flaviviridae family retrieved from NCBI Database. The studied parameters include Sequence alignment, prediction of condensed primers and Homology modeling construction. The Clustal series of programs are widely used in molecular biology for the multiple sequence alignment and for constructing phylogenetic trees from nucleotide sequences. Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR) process. Primer-BLAST offers adaptable choices to change the specificity threshold and other properties. This tool is useful to predict conserved primers in nucleotide query sequence. Three-dimensional structure of protein predicted by using Homology modeling study. This homology modeling prediction performed by a webtool Swiss model that uses amino acid sequences as an input query in workspace. This modeling study provides valuable information about 3D structure of models and their target template sequence alignment as well model coordination. In this pursuit, all the prediction studied parameters proceeds in silico.

Keywords: Homology modeling, NCBI database, Primer-BLAST, Sequence alignment.