find_kinase_consensus_in_proteins

find_kinase_consensus_in_proteins.R

## Find a kinase (here ABL1) consensus sequence in protein sequences using R.
proteins <- c("P00519", "P46109", "P61769") # ABL1, CRKL, B2M
for (ii in proteins) {
  prot_url <- paste("http://www.uniprot.org/uniprot/", ii, ".fasta", sep="") # url of protein fasta
  protein_fasta <- scan(file=url(prot_url), what="character", sep="\t")  # read the protein fasta
  protein_seq <- paste(protein_fasta[2:length(protein_fasta)], collapse="") # amino acid sequence only
  # print(protein_seq)
    for (ik in which(strsplit(protein_seq, '')[[1]]=='Y')) {
      tyr_context <- substr(protein_seq, ik-1, ik+3)
      # print(tyr_context)
      # search for ABL1 specific sequence:  I/V/L-Y-X-X-P/F:
      x <- grep(pattern = "[IVL]Y..[PF]", x = tyr_context, value = TRUE)
      if (length(x)!=0) {
        print(paste(ii, ": ", x, sep=""))
      }
    }
}

# Homework:
# 1) Try to search through protein_seq directly (don't use strsplit by Y).
# 2) Find other Tyr or Ser/Thr kinases target sequences.
# 3) Convert Uniprot ids to gene symbols.