- Follow ( http://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.
- Install the SeqinR package.
- To load “SeqinR” R package follow > library("seqinr")
- To write a sequence to a FASTA-format file in R, use “write.fasta()”function from the SeqinR R package.
- Name the output file using the “file.out” argument (input).
- Read FASTA format file into R using the read.fasta() function from the SeqinR package.
- 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")
- To read this FASTA format file follow > library("seqinr")
> dengue <- read.fasta(file = "den1.fasta")
- “den1.fasta” must be saved in the “My Documents” folder of the user’s PC.
Procedure to work the simulator
- A default FASTA file is available on the R platform.
- 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
- 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.
- Follow the code in the command window:
library("seqinr") # This line importing the seqinr library
dnaseq<- read.fasta(file = "sequence.fasta")
- Click Execute Button for output.