Nothing
SeqAna <- function(file,blastdb,nthread="8",mtras="1",..){
##### Blast
command1 <- paste("makeblastdb -in",blastdb,"-dbtype prot")
system(command1)
command2 <- paste("blastp -query",file,"-db",blastdb,"-num_threads",nthread,"-max_target_seqs",mtras,"-outfmt 6")
output <- system(command2,intern=TRUE)
output<- strsplit(output,"\t")
output <- do.call(rbind.data.frame,output)
colnames(output) <- c("QueryID","SubjectID","Pidentity","AligLength","Mismatch","GapOpening","Q-Start","Q-End","s-Start","s-end","Evalue","bit")
##### SignalP to predict signal peptide
command3 <- paste("signalp -f short",file)
sigpep <- system(command3,intern=TRUE)
sigpep1 <- strsplit(sigpep, " +")
sigpep1 <- do.call(rbind.data.frame,sigpep1)
colnames(sigpep1) <- c("name","Cmax","pos","Ymax","pos","Smax","pos","Smean","D","?","Dmaxcut","Networks-used")
sigpep1 <- sigpep1[-c(1:2), ]
sigpep1 <- sigpep1[, -13]
#rownames(sigpep1) <- sigpep1$name
###tmHMM
#command4 <- paste("tmhmm --short",file)
#tmout <- system(command4,intern=TRUE)
#tmout1<- strsplit(tmout,"\t")
#tmout1 <- do.call(rbind.data.frame,tmout1)
#colnames(tmout1) <- c("Id","Length","ExpectNoAA","First60","PredTranHelix","Topology")
#rownames(tmout1) <- tmout1$Id
### Hmm to identify protein domain
comnd5 <- paste("hmmpress",db)
system(comnd5)
command5 <- paste("hmmscan --cpu 2 --domtblout TrinotatePFAM.out",db,file)
hmout <- system(command5,intern=TRUE)
hmout1<- strsplit(hmout,"\t")
hmout1 <- do.call(rbind.data.frame,hmout1)
new("SequnecAnalysisData",Homologus=output,signalPeptide=sigpep1,HMM=hmout1)
}
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