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Example of genotyping analysis using combined approach

In this approach the uploaded sequence is given as an input to all the three methods, BLAST-, Phylogeny- and RTD-based for genotyping.

The methods are run in sequential manner and their output is displayed one below the other. The working examples of these individual approaches

are detailed as following,

A. Example of BLAST-based genotyping:

   1. Input sequences in fasta format in text area or browse the file. (Sample input file in fasta format, input.txt)

   2. Sequences will be uploaded.

   3. Assignment of genotype to input sequences that of closest reference sequence in terms of percent identity. 

   4. Get the predicted genotype of input sequences. (Sample output of BLAST search result )

B. Example of Phylogeny-based genotyping:

   1. Input sequences in fasta format in text area or browse the file. (Sample input file in fasta format, input.txt)

   2. Sequence will be uploaded. 

   3. Run the N-J phylogenetic analysis of query sequence(s) with reference genotypes.

   4. Obtain alignment file and phylogenetic tree.(Sample output file for alignment fasta.aln and N-J phylogeneic tree tree.dnd )

C. Example of RTD based genotyping:

   1. Input sequences in fasta format in text area or browse the file. (Sample input file in fasta format, input.txt)

   2. Sequence will be uploaded. 

   3. Compute the RTDs in input sequence(s) at k=4.

   4. Compute the distance of inpute sequence from reference sequence using RTD-based distance function.

   5. Output the predicted genotype of closest reference sequence for input sequence. (Sample output of BLAST search result )