# Function to return positions of glycosylation sites in amino acid sequences
FindGlyc <- function(
   AASeq, # list of amino acid sequences
   CapitalLetters = T, # Indicator for whether amino acids are in capital letters
   BlankSign = "-" # Sign for blanks
) {
   
   # Determine amino acids required at position x and x + 2 and not allowed at
   # x + 1
   if(CapitalLetters) {
      GlycMotiv1    <- c("N", "T") 
      GlycMotiv2    <- c("N", "S")
      GlycNotMiddle <- "P"
   } else {
      GlycMotiv1    <- c("n", "t") 
      GlycMotiv2    <- c("n", "s")
      GlycNotMiddle <- "p"
   } 
      
   sapply(AASeq, function(x) {# Loop through sequences
         
      # Indicators for all "non-blanks"
      NoBlankIndices <- x != BlankSign
         
      if (sum(NoBlankIndices) > 2) {
            
         # Indices of all positions within a sequence
         PosIndices <- seq_along(x)
            
         # Positions without blank sign
         PosIndices <- PosIndices[NoBlankIndices]
            
         # Amino acid sequence with blanks removed
         Seq <- x[NoBlankIndices]
            
         # Loop through sequenced amino acids and determine all positions 
         # with NXT or NXS sequence where X can be anything but P
         GlyInd <- sapply(1:(length(Seq) - 2), function(y) {
            all(Seq[c(y,(y + 2))] == GlycMotiv1 | Seq[c(y, (y + 2))] == GlycMotiv2 &
               rep(Seq[y + 1] != GlycNotMiddle, 2))
         })
            
         # Select position indices of original sequence that fulfill the 
         # above requirement of a glycosylation motiv
         PosIndices[which(GlyInd)]
      
      } # End of if
   }) # End of sapply
} # End of function

# Function to return positions of blanks in amino acid sequences
FindBlank <- function(
   AASeq, # list of amino acid sequences
   BlankSign = "-" # Sign for blanks
) {         
   sapply(AASeq, function(x) {# Loop through sequences
         
      # Indicators for all "blanks"
      which(x == BlankSign)
   }) # End of sapply
} # End of function