Package 'cleaver'

Title: Cleavage of Polypeptide Sequences
Description: In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html
Authors: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <[email protected]>
License: GPL (>= 3)
Version: 1.45.0
Built: 2024-10-31 05:52:45 UTC
Source: https://github.com/bioc/cleaver

Help Index

Cleavage of polypeptide sequences

Description

This package cleaves polypeptide sequences. It provides three functions: cleave, cleavageRanges and cleavageSites.

Details

The cleavage rules are taken from: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Package: cleaver
License: GPL (>= 3)
URL: https://github.com/sgibb/cleaver/

Author(s)

Sebastian Gibb [email protected]

References

https://github.com/sgibb/cleaver/

Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; "Protein Identification and Analysis Tools on the ExPASy Server". (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005).
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

See Also

cleave, cleavageRanges and cleavageSites.

Cleavage of polypeptide sequences

Description

This functions cleave polypeptide sequences. Use cleavageSites to find the cleavage sites, cleavageRanges to find the cleavage ranges and cleave to get the cleavage products.

Usage

## S4 method for signature 'character'
cleave(x, enzym = "trypsin", missedCleavages = 0,
                             custom = NULL, unique = TRUE)

## S4 method for signature 'AAString'
cleave(x, enzym = "trypsin", missedCleavages = 0,
                            custom = NULL, unique = TRUE)

## S4 method for signature 'AAStringSet'
cleave(x, enzym = "trypsin", missedCleavages = 0,
                               custom = NULL, unique = TRUE)

## S4 method for signature 'character'
cleavageRanges(x, enzym = "trypsin", missedCleavages = 0,
                                     custom = NULL)

## S4 method for signature 'AAString'
cleavageRanges(x, enzym = "trypsin", missedCleavages = 0,
                                    custom = NULL)

## S4 method for signature 'AAStringSet'
cleavageRanges(x, enzym = "trypsin", missedCleavages = 0,
                                       custom = NULL)

## S4 method for signature 'character'
cleavageSites(x, enzym = "trypsin", custom = NULL)

## S4 method for signature 'AAString'
cleavageSites(x, enzym = "trypsin", custom = NULL)

## S4 method for signature 'AAStringSet'
cleavageSites(x, enzym = "trypsin", custom = NULL)

Arguments

x

polypeptide sequences.
enzym

character, cleavage rule.
missedCleavages

numeric, number of missed cleavages.
custom

character, of length 1 or 2. Could be used to define own cleaveage rules. The first element would be the pattern and the optional second element would be an exception (non-cleavage) pattern. Perl-like regular expressions are supported, see gregexpr for details. If custom is set the enzym is ignored.
unique

logical, if TRUE all duplicated cleavage products per peptide are removed.

Details

The cleavage rules are taken from: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

Cleavage rules (cleavage between P1 and P1'):

Rule name P4 P3 P2 P1 P1' P2'
arg-c proteinase - - - R - -
asp-n endopeptidase - - - - D -
bnps-skatole-c - - - W - -
caspase1 F,W,Y,L - H,A,T D not P,E,D,Q,K,R -
caspase2 D V A D not P,E,D,Q,K,R -
caspase3 D M Q D not P,E,D,Q,K,R -
caspase4 L E V D not P,E,D,Q,K,R -
caspase5 L,W E H D - -
caspase6 V E H,I D not P,E,D,Q,K,R -
caspase7 D E V D not P,E,D,Q,K,R -
caspase8 I,L E T D not P,E,D,Q,K,R -
caspase9 L E H D - -
caspase10 I E A D - -
chymotrypsin-high - - - F,Y not P -
- - - W not M,P -
chymotrypsin-low - - - F,L,Y not P -
- - - W not M,P -
- - - M not P,Y -
- - - H not D,M,P,W -
clostripain - - - R - -
cnbr - - - M - -
enterokinase D,E D,E D,E K - -
factor xa A,F,G,I,L,T,V,M D,E G R - -
formic acid - - - D - -
glutamyl endopeptidase - - - E - -
granzyme-b I E P D - -
hydroxylamine - - - N G -
iodosobenzoic acid - - - W - -
lysc - - - K - -
lysn - - - - K -
lysarginase - - - - K,R -
neutrophil elastase - - - A,V - -
ntcb - - - - C -
pepsin1.3 - not H,K,R not P not R F,L not P
pepsin - not H,K,R not P not R F,L,W,Y not P
- not H,K,R not P F,L,W,Y - not P
- not H,K,R not P F,L - not P
proline endopeptidase - - not H,K,R P not P -
proteinase k - - - A,E,F,I,L,T,V,W,Y - -
staphylococcal peptidase i - - not E E - -
thermolysin - - - not D,E A,F,I,L,M,V -
thrombin - - G R G -
A,F,G,I,L,T,V,M A,F,G,I,L,T,V,W P R not D,E not D,E
trypsin - - - K,R not P -
- - W K P -
- - M R P -
trypsin-high - - - K,R not P -
- - W K P -
- - M R P -
trypsin-low - - - K,R not P -
- - W K P -
- - M R P -
trypsin-simple - - - K,R - -

Exceptions:

Rule name Enzyme name P4 P3 P2 P1 P1' P2'
trypsin - - C,D K D -
- - C K H,Y -
- - C R K -
- - R R H,R -
trypsin-high - - C,D K D -
- - C K H,Y -
- - C R K -
- - R R H,R -
Rule name Enzyme name
arg-c proteinase Arg-C proteinase
asp-n endopeptidase Asp-N endopeptidase
bnps-skatole-c BNPS-Skatole
caspase1 Caspase 1
caspase2 Caspase 2
caspase3 Caspase 3
caspase4 Caspase 4
caspase5 Caspase 5
caspase6 Caspase 6
caspase7 Caspase 7
caspase8 Caspase 8
caspase9 Caspase 9
caspase10 Caspase 10
chymotrypsin-high Chymotrypsin-high specificity (C-term to [FYW], not before P)
chymotrypsin-low Chymotrypsin-low specificity (C-term to [FYWML], not before P)
clostripain Clostripain (Clostridiopeptidase B)
cnbr CNBr
enterokinase Enterokinase
factor xa Factor Xa
formic acid Formic acid
glutamyl endopeptidase Glutamyl endopeptidase
granzyme-b Granzyme B
hydroxylamine Hydroxylamine
iodosobenzoic acid Iodosobenzoic acid
lysc LysC
lysn LysN
lysarginase LysargiNase
neutrophil elastase Neutrophil elastase
ntcb NTCB (2-nitro-5-thiocyanobenzoic acid)
pepsin1.3 Pepsin (pH == 1.3)
pepsin Pepsin (pH > 2)
proline endopeptidase Proline-endopeptidase
proteinase k Proteinase K
staphylococcal peptidase i Staphylococcal Peptidase I
thermolysin Thermolysin
thrombin Thrombin
trypsin Trypsin
trypsin-high Trypsin, higher specificity as defined in PeptideMass, identical to trypsin
trypsin-low Trypsin, C-term to K/R if C-term is not P, as defined in PeptideMass
trypsin-simple Trypsin, C-term to K/R, even before P, as defined in PeptideMass

Value

cleave

If x is a character it returns a list of the same length as x. Each element contains a character vector with the corresponding cleavage products of the polypeptides. If x is an AAString or an AAStringSet an AAStringSet or an AAStringSetList instance of the same length as x is returned. Each element contains an AAString or an AAStringSet instance with the corresponding cleavage products of the polypeptides.

cleavageRanges

If x is a character it returns a list of the same length as x. Each element contains a two-column matrix with the start and end positions of the peptides. If x is an AAString or an AAStringSet instance an IRanges or an IRangesList of the same length as x is returned.

cleavageSites

Returns a list of the same length as x. Each element contains an integer vector with the cleavage positions.

Overview:

Input cleave cleavageRanges cleavageSites
character list of character list of matrix list of integer
AAString AAStringSet IRanges list of integer
AAStringSet AAStringSetList IRangesList list of integer

Author(s)

Sebastian Gibb <[email protected]>

References

Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; "Protein Identification and Analysis Tools on the ExPASy Server". (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005).
https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

PeptideMass https://web.expasy.org/peptide_mass/peptide-mass-doc.html#table1

See Also

AAString, AAStringSet, AAStringSetList, IRanges, IRangesList

Examples

library("cleaver")

## Gastric juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358)
gaju <- "LAAGKVEDSD"

cleave(gaju, "trypsin")
# $LAAGKVEDSD
# [1] "LAAGK" "VEDSD"

cleavageRanges(gaju, "trypsin")
# $LAAGKVEDSD
#      start end
# [1,]     1   5
# [2,]     6  10

cleavageSites(gaju, "trypsin")
# $LAAGKVEDSD
# [1] 5

cleave(gaju, "trypsin", missedCleavages=1)
# $LAAGKVEDSD
# [1] "LAAGKVEDSD"

cleavageRanges(gaju, "trypsin", missedCleavages=1)
# $LAAGKVEDSD
#      start end
# [1,]     1  10

cleave(gaju, "trypsin", missedCleavages=0:1)
# $LAAGKVEDSD
# [1] "LAAGK" "VEDSD" "LAAGKVEDSD"

cleavageRanges(gaju, "trypsin", missedCleavages=0:1)
# $LAAGKVEDSD
#      start end
# [1,]     1   5
# [2,]     6  10
# [3,]     1  10


cleave(gaju, "pepsin")
# $LAAGKVEDSD
# [1] "LAAGKVEDSD"
# (no cleavage)


## use AAStringSet
gaju <- AAStringSet("LAAGKVEDSD")

cleave(gaju)
# AAStringSetList of length 1
# [["LAAGKVEDSD"]] LAAGK VEDSD


## Beta-enolase (UniProtKB/Swiss-Prot: ENOB_THUAL/P86978)
enob <- "SITKIKAREILD"

cleave(enob, "trypsin")
# $SITKIKAREILD
# [1] "SITK" "IK"   "AR"   "EILD"

cleave(enob, "trypsin", missedCleavages=2)
# $SITKIKAREILD
# [1] "SITKIKAR" "IKAREILD"

cleave(enob, "trypsin", missedCleavages=0:2)
# $SITKIKAREILD
# [1] "SITK"     "IK"       "AR"       "EILD"     "SITKIK"   "IKAR"
# [7] "AREILD"   "SITKIKAR" "IKAREILD"

## define own cleavage rule: cleave at K
cleave(enob, custom="K")
# $SITKIKAREILD
# [1] "SITK"   "IK"     "AREILD"

cleavageRanges(enob, custom="K")
# $SITKIKAREILD
#      start end
# [1,]     1   4
# [2,]     5   6
# [3,]     7  12

## define own cleavage rule: cleave at K but not if followed by A
cleave(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
# [1] "SITK"     "IKAREILD"

cleavageRanges(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
#      start end
# [1,]     1   4
# [2,]     5  12

cleavageSites(enob, custom=c("K", "K(?=A)"))
# $SITKIKAREILD
# [1] 4