Reading FASTA using SequinR

  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.
  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 R 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

  4. A default FASTA file is available on the R platform.

  5. User can choose their required sequence and can load the sequence.fasta file into the platform.

    Fig.1. Platform for writing and reading FASTA format in R

  6. 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.

  7. Follow the code in the command window: library("seqinr")# This line importing the seqinr library dnaseq<- read.fasta(file = "sequence.fasta") `

  8. Click Execute Button for output.