2.3.1 ǀ Sequence retrieval and Physico-chemical parameters of
cpOAS1
The submitted and published cpOAS1 (Acc No MN564841) template from the
present study was used for bioinformatics analysis. This template was
blasted against the PDB database using Blast P in NCBI Blast, using
default parameters. Monomer porcine (PDB ID: 4rwp) template was selected
based on maximum identity among the amino acids, e-value, query coverage
and other properties. This template was used for predicting the 3-D
structure of the cpOAS1 protein. ProtParam tool of ExPASy, SIB
Bioinformatics resource portal (http://web.expasy.org/protparam/),
was used to compute the basic Physico-chemical properties of cpOAS1 like
molecular weight, theoretical isoelectric point (pI), the total number
of positive (Asp + Glu) and negative residues(Arg + Lys), formula,
number of atoms, extinction coefficient (EC)28,
estimated half-life29, instability index
(II)30, aliphatic index (AI;)31 and
grand average hydropathy (GRAVY)32. The Kyte-Doolittle
scale was used for detecting hydrophobic regions in the cpOAS1 proteins.
Regions with positive and negative values are depicted as hydrophobic
and hydrophilic, respectively. Under this scale, the window size was
kept at 9, the relative weight for window edges was 100 % and the
linear weighted variation model was selected. Hydrophobicity was
computed by the ProtScale.