Procedure to work simulator

1. Consider three random protein sequences: Protein Sequence 1, Protein Sequence 2, Protein Sequence 3.

 

.fasta format aminoacid sequences were aligned using multiple sequence alignment with sequinR package. The dist.alignment() function takes a multiple alignment as input and calculates calculates the genetic distance between each pair of proteins in the multiple alignment.  

2. Click on run button to execute simulator.

 

The numerical values in matrix of the output indicates genetic distance between each pair of proteins in the multiple alignment. The larger the genetic distance between two sequences, the more amino acid changes or indels that have occurred since they shared a common ancestor, and the longer ago their common ancestor probably lived.

 

DIY

 

1. Follow ( https://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.

2. Install the SeqinR package.

   Import “seqinr” library to R workspace

3. Create a function() for retrieving multiple sequence from database

   Function 1

    create a list to store sequences
           
            connect to the database
           
            for each element in the array query the sequence and assign to a variable 
                
            append the data into a list
                
            end
                
            close the connection
                
            return list
           
            end of fuction 1
           

4. Create a vector of sequences

5. Retrieve the sequences from the database

6. Write the sequences into a file

7. Align the sequence and assign to a variable in phylip format