fragmentSeq: Fragment Protein Or Peptide Sequence

Description

Makes internal/terminal fragments of a SINGLE peptide/protein input (as single letter amino-acid code) and returns list of all possible sequences ($full, $Nter, $Cter, $inter).

Usage

fragmentSeq(
  sequ,
  minSize = 3,
  maxSize = 300,
  internFragments = TRUE,
  separTerm = FALSE,
  keepRedSeqs = TRUE,
  prefName = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a numeric vector with the (neutral) mass of fragmented peptides

Arguments

sequ: (character, length=1) sequence used for fragmenting, as as mono-aminoacid letter code (so that cuting will be perfomed between all the letters/characters)
minSize: (integer) min number of AA residues for considering peptide fragments
maxSize: (integer) max number of AA residues for considering peptide fragments
internFragments: (logical) logical (return only terminal fragments if 'FALSE')
separTerm: (logical) if 'TRUE', separate N-terminal, C-terminal and internal fragments in list
keepRedSeqs: (logical) if 'FALSE' remove fragments with redundant content (but my be from different origin in 'sequ'); remove redundant so far only when no separation of Nterm/Cterm/intern as list
prefName: (logical) alternative name for all fragments (default the sequence itself), avoid separators '.' and '-'
silent: (logical) suppress messages
debug: (logical) additional messages for debugging
callFrom: (character) allow easier tracking of messages produced

Details

Note: Thus function can handle only 1 sequence at each run ! Note: The mass values returned correspond to neutral peptides. If you are looking for ions, you need to adjust masses to the repsective ion-charcteriostics (adding H+, etc).

Examples

Run this code

fragmentSeq("ABCDE")
fragmentSeq("ABCDE", minSize=3, internFragments=FALSE)
fragmentSeq("ABCDE", minSize=3, internFragments=TRUE)

## Run multiple peptides/proteins
twoPep <- cbind(c("a","ABCABCA"), c("e","EFGEFGEF"))
apply(twoPep, 2, function(x) fragmentSeq(x[2], mi=3, kee=FALSE, sep=TRUE, pre=x[1]))

## Ubiquitin example
P0CG48 <- "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"  
system.time( fra1 <- (fragmentSeq(P0CG48, mi=5, kee=FALSE)))      # < 0.5 sec