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Pipeline publication

[…] dian strains (Bangalore-CAA88227.1, Bangalore (Ban4)-AAD51286.1, Bangalore (Ban5)-AAK19178.1, Bangalore (Kolar)-AAL26553.1, Varanasi-AAO25668.1, Kelloo-AAM21566.1, Karnataka-AAB08929.1, New Delhi (Mild)-AAA92817.1, and Lucknow-CAA76209.1) were also obtained for multiple sequence alignment and phylogenetic analysis., The family of coat protein was studied using a combination of programs, namely, NCBI CD- Search (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, database searched: CDD v3.03–42251 PSSMs) [], PSI-BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) [], and Pfam (http://pfam.sanger.ac.uk/) []. CD-Search is a NCBI's interface to search Conserved Domain Database (CDD) which utilizes RPS-BLAST (Reverse-PSI-BLAST; a variant of PSI-BLAST) to scan a set of precalculated position specific scoring matrices (PSSMs) using a protein query. PSI-BLAST (position-specific-iterated BLAST) uses initial matches to query sequence to build scoring matrix and appends additional matches to the matrix by an iterative search method in order to detect remote homologs. Pfam designates protein family by HMM (Hidden Markov Model)-based search (default settings were chosen and Pfam-A significant matches were only considered) over known protein family classifiers., Nuclear localization signals (NLSs) were predicted using cNLS Mapper (http://nls-mapper.iab.keio.ac.jp/) [] as coat protein that is known to be karyophilic []. cNLS Mapper is a computer program that predicts NLS by activity-based profile search and an additivity-based motif scoring function in different classes of importin-α/β pathway-specific NLS. The prediction was made with a score cut-off of 5.0 and searched for both mono- and bipartite NLSs with a long linker (13–20 amino acid length) as ToLCGV possesses mono-bipartite genome organization []. Classic NLS typically rich in basic amino acids such as lysine and arginine, the counts of basic amino acids was performed manually in the above predicted NLSs. Comparison with literature-reported NLS sp […]

Pipeline specifications

Software tools BLASTN, BLASTP, cNLS Mapper
Databases CDD