How to use RV-Typer?

  1. RV-Typer performs the prediction of Rhinovirus serotypes using VP1 sequence(s). Please enter protein or nucleotide sequences consisting of VP1 region in fasta format in text area or upload the text file and submit the form. (Sample input file in fasta format: Protein, Nucleotide)

  2. Based on type of sequences selected (protein/nucleotide), BLASTP or BLASTX search will be performed against database of VP1 protein sequences of reference serotypes of RV - A, -B and -C. The sequence corresponding to VP1 region will be extracted for each input protein sequence or translated input nucleotide sequence using BLAST search.

  3. The server will then compute return time distributions (RTDs) of VP1 protein sequence(s) at k = 2.

  4. The distance(s) of input VP1 sequence(s) from reference VP1 sequences will be calculated using RTD-based Euclidean type distance function.

  5. The result for the serotype prediction for input sequence(s) will be displayed. (Sample output result )

Note: Sequences having low/no similarity with reference sequences and which do not meet RTD-based distance cut-off criteria will not be assigned to any serotype. In these cases, such notification will be displayed in the result.