Package cleaver. August 2, 2013
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1 Package cleaver August 2, 2013 Version Date Title Cleavage of polypeptide sequences Maintainer Sebastian Gibb Depends R (>= 3.0.0), methods, Biostrings (>= ) Imports IRanges Suggests testthat, knitr, BiocStyle (>= ), BRAIN, UniProt.ws (>= 2.1.4) Description In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: License GPL (>= 3) URL BugReports LazyLoad yes VignetteBuilder knitr biocviews Bioinformatics, Proteomics Author Sebastian Gibb [aut, cre] R topics documented: cleaver-package cleave Index 7 1
2 2 cleave cleaver-package Cleavage of polypeptide sequences Description Details This package cleaves polypeptide sequences. It provides only one function: cleave The cleavage rules are taken from: enzymes.html Package: cleaver License: GPL (>= 3) URL: Author(s) Sebastian Gibb 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). See Also cleave cleave Cleavage of polypeptide sequences Description This function cleaves polypeptide sequences.
3 cleave 3 Usage ## S4 method for signature character cleave(x, enzym = "trypsin", missedcleavages = 0) ## S4 method for signature AAString cleave(x, enzym = "trypsin", missedcleavages = 0) ## S4 method for signature AAStringSet cleave(x, enzym = "trypsin", missedcleavages = 0) Arguments x Details polypeptide sequences. enzym character, cleavage rule. missedcleavages numeric, number of missed cleavages. The cleavage rules are taken from: enzymes.html Cleavage rules (cleavage between P1 and P1 ): Rule name P4 P3 P2 P1 P1 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 -
4 4 cleave glutamyl endopeptidase D - 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,W,Y - not H,K,R not P F,L,W,Y - pepsin - not H,K,R not P not R F,L - not H,K,R not P F,L - 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 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)
5 cleave 5 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 Value a list of splitted polypeptides if input x was a character or a AAStringSetList if input x was an AAStringSet). Author(s) Sebastian Gibb 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). See Also AAString, AAStringSet, AAStringSetList Examples library("cleaver") ## Gastic juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358) gaju <- "LAAGKVEDSD"
6 6 cleave cleave(gaju, "trypsin") # [1] "LAAGK" "VEDSD" cleave(gaju, "trypsin", missedcleavages=1) # [1] "LAAGKVEDSD" cleave(gaju, "trypsin", missedcleavages=0:1) # [1] "LAAGK" "VEDSD" "LAAGKVEDSD" cleave(gaju, "pepsin") # [1] "LAAGKVEDSD" # (no cleavage) ## use AAStringSet gaju <- AAStringSet("LAAGKVEDSD") cleave(gaju) # AAStringSetList of length 1 # [["LAAGKVEDSD"]] LAAGK VEDSD LAAGKVEDSD
7 Index Topic methods cleave, 2 Topic package cleaver-package, 2 AAString, 5 AAStringSet, 5 AAStringSetList, 5 cleave, 2, 2 cleave,aastring-method (cleave), 2 cleave,aastringset-method (cleave), 2 cleave,character-method (cleave), 2 cleaver-package, 2 7
Package cleaver. December 13, 2018
Version 1.20.0 Date 2017-06-08 Title Cleavage of Polypeptide Sequences Package cleaver December 13, 2018 Maintainer Sebastian Gibb Depends R (>= 3.0.0), methods, Biostrings (>=
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1. Using phylogeny all living organisms can be divided into the following domains: A. Bacteria, Eukarya, and Vertebrate B. Archaea and Eukarya C. Bacteria, Eukarya, and Archaea D. Eukarya and Bacteria
Package R1magic. August 29, 2016
Type Package Package R1magic August 29, 2016 Title Compressive Sampling: Sparse Signal Recovery Utilities Version 0.3.2 Date 2015-04-19 Maintainer Depends stats, utils Utilities
SERVA ICPL Kit (Cat.-No )
INSTRUCTION MANUAL SERVA ICPL Kit (Cat.-No. 39230.01) SERVA Electrophoresis GmbH Carl-Benz-Str. 7 D-69115 Heidelberg Phone +49-6221-138400, Fax +49-6221-1384010 e-mail: info@serva.de http://www.serva.de
Package svydiags. June 4, 2015
Type Package Package svydiags June 4, 2015 Title Linear Regression Model Diagnostics for Survey Data Version 0.1 Date 2015-01-21 Author Richard Valliant Maintainer Richard Valliant Description