fragmentSeq {wrTopDownFrag}

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,
  callFrom = NULL
)

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

callFrom

(character) allow easier tracking of message(s) produced

Value

numeric vector with mass

See Also

makeFragments; convAASeq2mass

Examples

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