Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ## 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)
|
x |
polypeptide sequences. |
enzym |
|
missedCleavages |
|
custom |
|
unique |
|
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 | - |
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 | - | |
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 | - | ||
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 |
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 |
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 |
Sebastian Gibb <mail@sebastiangibb.de>
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
AAString
,
AAStringSet
,
AAStringSetList
,
IRanges
,
IRangesList
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | 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
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