Procedure

 

1. Follow ( http://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.
2. Install the SeqinR package.
3. To load “SeqinR” R package follow > library("seqinr") 
4. To write a sequence to a FASTA-format file in R, use “write.fasta()”function from the SeqinR R package.
5. Name the output file using the “file.out” argument (input).
6.  Read FASTA format file into R using the read.fasta() function from the SeqinR package.

 

Example

 

1. If a user stored DEN-1 Dengue virus sequence in a vector dengueseq, for writing the sequence to a FASTA-format file called “den1.fasta” that contains the sequence labelled as “DEN-1”, follow                                                                                                                                      > write.fasta(names="DEN-1", sequences=dengueseq, file.out="den1.fasta")
2. To read this FASTA format file follow                                                                                                                                                                         > library("seqinr")
                           > dengue <- read.fasta(file = "den1.fasta")
3. “den1.fasta” must be saved in the “My Documents” folder of the user’s PC.

 

 

Procedure to work the simulator

 

1.  A default FASTA file is available on the R platform.
2. User can choose their required sequence and can load the sequence.fasta file into the platform.                                                     Figure.1. Platform for writing and reading FASTA format in R                                                                                                                                                                                    
3.   In case of sequence files other than FASTA file, user have to upload the file and rewrite the name sequence.fasta" into filename.fasta format.
4. Follow the code in the command window: 
                               library("seqinr") # This line importing the seqinr library 
                               dnaseq<- read.fasta(file = "sequence.fasta")   
5. Click Execute Button for output.