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. Follow the code in the command window:
retrieveseqs<- function(seqnames,acnucdb) #custom function for retrieving multiple sequence from Uniprot
{
myseqs<- list()
# Make a list to store the sequences
require("seqinr")
choosebank(acnucdb)
for (i in 1:length(seqnames))
{
seqname<- seqnames[i]
print(paste("Retrieving sequence",seqname,"..."))
queryname<- "query2"
query<- paste("AC=",seqname,sep="")
query_test<- query(queryname,`query`)
seq<- getSequence(query_test$req[[1]]) # Makes a vector "seq" containing the sequence
myseqs[[i]] <- seq
}
closebank()
return(myseqs)
}
seqnames<- c("P06747", "P0C569", "O56773", "Q5VKP1")
seqs<- retrieveseqs(seqnames,"swissprot")
length(seqs)
seq1 <- seqs[[1]]
seq1
seq2 <- seqs[[2]]
seq2[1:20]
Procedure to work simulator
- To retrieve sequence information of a list of proteins, user can enter the known accession number of proteins of interest in the search box. List the accession numbers of proteins with a space in between the accession numbers.
![](https://vlab.amrita.edu/userfiles/1/1632121381_2.jpg)
For example, in this simulator accession numbers of some proteins are given. Q9CD83, P06747, O56773, Q5VKP1).
Provide the sample accession numbers and click on Run button to execute simulation.
![](https://vlab.amrita.edu/userfiles/1/1632121583_3.jpg)
- The result page displays information of list of proteins related to the query search.
- User can try to run the simulator with other accession numbers Q14533, Q9BYR3, P26371, Q07627, Q3TTY5.