Procedure to work the simulator

 

1. Enter Accession number in the query box provided in the platform. An accession number in bioinformatics indicates a unique identifier given to a DNA or protein sequence for tracking of different versions of that sequence record and the associated sequence over time in a single data repository.

    

2. Click on Run button to execute simulation.

    

The complete genome sequence of the particular organism is displayed as result.

 

Note

This experiment retrieves the sequence data directly from the NCBI database using R programming. Using the choosebank() function in the ‘seqinr’ library the R platform connects to the GenBank database. Using the R programming, user can retrieve and save the species specific sequence data in a variable.

 

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.

3. To load “SeqinR” R package follow > library("seqinr")

4. For retrieving a specific sequence with particular NCBI accession, use R function “getncbiseq()”.

  > getncbiseq <- function(accession) { require("seqinr") # this function requires the SeqinR R package`

  first find which ACNUC database the accession is stored in:

    dbs <- c("genbank","refseq","refseqViruses","bacterial")
            numdbs <- length(dbs)
            for (i in 1:numdbs)
            {
            db <- dbs[i]
            choosebank(db)
        

check if the sequence is in ACNUC database 'db':

    resquery <- try(query(".tmpquery", paste("AC=", accession)), silent = TRUE)
            if (!(inherits(resquery, "try-error")))
            {
            queryname <- "query2"
            thequery <- paste("AC=",accession,sep="")
            query(`queryname`,`thequery`)
        

see if a sequence was retrieved:

    seq <- getSequence(query2$req[[1]])
            closebank()
            return(seq)
            }
            closebank()
            }
            print(paste("ERROR: accession",accession,"was not found"))
            }
        

 

EXAMPLE • After entering function getncbiseq() into R, retrieve a sequence from the NCBI Nucleotide database, for example accession NC_001477.

• Follow the code

    > dengueseq <- getncbiseq("NC_001477")
        

• Dengueseq variable is a vector containing the nucleotide sequence