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|
rebaseextract
Function
Extract data from REBASE
Description
The Restriction Enzyme database (REBASE) is a collection of
information about restriction enzymes and related proteins. It
contains published and unpublished references, recognition and
cleavage sites, isoschizomers, commercial availability, methylation
sensitivity, crystal and sequence data. DNA methyltransferases, homing
endonucleases, nicking enzymes, specificity subunits and control
proteins are also included. Most recently, putative DNA
methyltransferases and restriction enzymes, as predicted from analysis
of genomic sequences, are also listed.
The home page of REBASE is: http://rebase.neb.com/
This program derives recognition site and cleavage information from
the "withrefm" file of an REBASE distribution. It creates three files
in the EMBOSS data subdirectory REBASE. A pattern file, a reference
file and a supplier file.
It will also (by default) produce an 'embossre.equ' file. This can be
turned off by setting the -equivalences option to be false. This
option calculates an 'embossre.equ' file using restriction enzyme
prototypes in the "withrefm" file. The 'embossre.equ' file is a file
of preferred isoschizomers. You may edit it to contain your available
restriction enzymes.
The EMBOSS programs that find restriction cutting sites use the data
files produced by this program and will not work without them.
Running this program may be the job of your system manager.
Usage
Here is a sample session with rebaseextract
% rebaseextract
Extract data from REBASE
REBASE database withrefm file: withrefm
REBASE database proto file: proto
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-infile] infile REBASE database withrefm file
[-protofile] infile REBASE database proto file
Additional (Optional) qualifiers:
-[no]equivalences boolean [Y] This option calculates an embossre.equ
file using restriction enzyme prototypes in
the withrefm file.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers: (none)
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
Input file format
The input file must be the "withrefm" file of a REBASE distribution.
For example, the withrefm file for REBASE version 005 is at:
ftp://ftp.neb.com/pub/rebase/withrefm.005
Input files for usage example
File: withrefm
REBASE version 106 withrefm.106
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
REBASE, The Restriction Enzyme Database http://rebase.neb.com
Copyright (c) Dr. Richard J. Roberts, 2001. All rights reserved.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Rich Roberts May 31 2001
<ENZYME NAME> Restriction enzyme name.
<ISOSCHIZOMERS> Other enzymes with this specificity.
<RECOGNITION SEQUENCE>
These are written from 5' to 3', only one strand being given.
If the point of cleavage has been determined, the precise site
is marked with ^. For enzymes such as HgaI, MboII etc., which
cleave away from their recognition sequence the cleavage sites
are indicated in parentheses.
For example HgaI GACGC (5/10) indicates cleavage as follows:
5' GACGCNNNNN^ 3'
3' CTGCGNNNNNNNNNN^ 5'
In all cases the recognition sequences are oriented so that
the cleavage sites lie on their 3' side.
REBASE Recognition sequences representations use the standard
abbreviations (Eur. J. Biochem. 150: 1-5, 1985) to represent
ambiguity.
R = G or A
Y = C or T
M = A or C
K = G or T
S = G or C
W = A or T
B = not A (C or G or T)
D = not C (A or G or T)
H = not G (A or C or T)
V = not T (A or C or G)
N = A or C or G or T
ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES:
Enzymes that cut on both sides of their recognition sequences,
such as BcgI, Bsp24I, CjeI and CjePI, have 4 cleavage sites
each instead of 2.
[Part of this file has been deleted for brevity]
<5>Klebsiella pneumoniae OK8
<6>ATCC 49790
<7>ABCDEFGHIJKLMNOQRSTU
<8>Kiss, A., Finta, C., Venetianer, P., (1991) Nucleic Acids Res., vol. 19, pp.
3460.
Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp.
343-353.
Tomassini, J., Roychoudhury, R., Wu, R., Roberts, R.J., (1978) Nucleic Acids Re
s., vol. 5, pp. 4055-4064.
<1>Ksp632I
<2>Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,Ear
I,TdeII,Uba1192I,Uba1276I,VpaKutEI,VpaKutFI,VpaO5I
<3>CTCTTC(1/4)
<4>
<5>Kluyvera species 632
<6>DSM 4196
<7>M
<8>Bolton, B.J., Schmitz, G.G., Jarsch, M., Comer, M.J., Kessler, C., (1988) Ge
ne, vol. 66, pp. 31-43.
Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides & Nucleo
tides, vol. 13, pp. 1617-1626.
<1>MaeII
<2>HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
<3>A^CGT
<4>
<5>Methanococcus aeolicus PL-15/H
<6>K.O. Stetter
<7>M
<8>Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O.,
Schmitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.
<1>NotI
<2>CciNI,CspBI,MchAI
<3>GC^GGCCGC
<4>?(4)
<5>Nocardia otitidis-caviarum
<6>ATCC 14630
<7>ABCDEFGHJKLMNOQRSTU
<8>Borsetti, R., Wise, D., Qiang, B.-Q., Schildkraut, I., Unpublished observati
ons.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Benner, J.S., Claus, T.E., US Patent Office, 1994.
Qiang, B.-Q., Schildkraut, I., (1987) Methods Enzymol., vol. 155, pp. 15-21.
<1>TaqI
<2>CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,Hpy
F30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF6
4I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,Tfi
Tok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D2
1I,TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
<3>T^CGA
<4>4(6)
<5>Thermus aquaticus YTI
<6>J.I. Harris
<7>ABCDEFGIJLMNOQRSTU
<8>Anton, B.P., Brooks, J.E., Unpublished observations.
Fomenkov, A., Xiao, J.-P., Dila, D., Raleigh, E., Xu, S.-Y., (1994) Nucleic Aci
ds Res., vol. 22, pp. 2399-2403.
McClelland, M., (1981) Nucleic Acids Res., vol. 9, pp. 6795-6804.
Sato, S., Hutchison, C.A. III, Harris, J.I., (1977) Proc. Natl. Acad. Sci. U. S
. A., vol. 74, pp. 542-546.
Zebala, J.A., (1993) Diss. Abstr., vol. 54, pp. 1394-1398.
File: proto
REBASE version 305 proto.305
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
REBASE, The Restriction Enzyme Database http://rebase.neb.com
Copyright (c) Dr. Richard J. Roberts, 2003. All rights reserved.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Rich Roberts Apr 30 2003
TYPE II ENZYMES
---------------
BseYI CCCAGC (-5/-1)
BsiYI CCNNNNN^NNGG
BsrI ACTGG (1/-1)
HaeIII GG^CC
HpaII C^CGG
Ksp632I CTCTTC (1/4)
MaeII A^CGT
TYPE I ENZYMES
---------------
EcoAI GAGNNNNNNNGTCA
EcoBI TGANNNNNNNNTGCT
EcoDI TTANNNNNNNGTCY
EcoDR2 TCANNNNNNGTCG
EcoDR3 TCANNNNNNNATCG
EcoDXXI TCANNNNNNNRTTC
EcoEI GAGNNNNNNNATGC
EcoKI AACNNNNNNGTGC
TYPE III ENZYMES
---------------
EcoPI AGACC
EcoP15I CAGCAG (25/27)
HinfIII CGAAT
StyLTI CAGAG
Output file format
Output files for usage example
Directory: REBASE
This directory contains output files, for example embossre.enz
embossre.equ embossre.ref and embossre.sup.
File: REBASE/embossre.enz
# REBASE enzyme patterns for EMBOSS
#
# Format:
# name<ws>pattern<ws>len<ws>ncuts<ws>blunt<ws>c1<ws>c2<ws>c3<ws>c4
#
# Where:
# name = name of enzyme
# pattern = recognition site
# len = length of pattern
# ncuts = number of cuts made by enzyme
# Zero represents unknown
# blunt = true if blunt end cut, false if sticky
# c1 = First 5' cut
# c2 = First 3' cut
# c3 = Second 5' cut
# c4 = Second 3' cut
#
# Examples:
# AAC^TGG -> 6 2 1 3 3 0 0
# A^ACTGG -> 6 2 0 1 5 0 0
# AACTGG -> 6 0 0 0 0 0 0
# AACTGG(-5/-1) -> 6 2 0 1 5 0 0
# (8/13)GACNNNNNNTCA(12/7) -> 12 4 0 -9 -14 24 19
#
# i.e. cuts are always to the right of the given
# residue and sequences are always with reference to
# the 5' strand.
# Sequences are numbered ... -3 -2 -1 1 2 3 ... with
# the first residue of the pattern at base number 1.
#
AaeI ggatcc 6 0 0 0 0 0 0
AciI CCGC 4 2 0 1 3 0 0
AclI AACGTT 6 2 0 2 4 0 0
BamHI GGATCC 6 2 0 1 5 0 0
BceAI ACGGC 5 2 0 17 19 0 0
Bsc4I CCNNNNNNNGG 11 2 0 7 4 0 0
Bse1I ACTGG 5 2 0 6 4 0 0
BseYI CCCAGC 6 2 0 1 5 0 0
BshI GGCC 4 2 1 2 2 0 0
BsiSI CCGG 4 2 0 1 3 0 0
BsiYI CCNNNNNNNGG 11 2 0 7 4 0 0
BssKI CCNGG 5 2 0 -1 5 0 0
BsrI ACTGG 5 2 0 6 4 0 0
Bsu6I CTCTTC 6 2 0 7 10 0 0
ClaI ATCGAT 6 2 0 2 4 0 0
EcoRI GAATTC 6 2 0 1 5 0 0
EcoRII CCWGG 5 2 0 -1 5 0 0
HaeIII GGCC 4 2 1 2 2 0 0
HhaI GCGC 4 2 0 3 1 0 0
Hin4I GAYNNNNNVTC 11 4 0 -9 -14 24 19
Hin6I GCGC 4 2 0 1 3 0 0
HinP1I GCGC 4 2 0 1 3 0 0
HindI cac 3 0 0 0 0 0 0
HindII GTYRAC 6 2 1 3 3 0 0
HindIII AAGCTT 6 2 0 1 5 0 0
HpaII CCGG 4 2 0 1 3 0 0
HpyCH4IV ACGT 4 2 0 1 3 0 0
HspAI GCGC 4 2 0 1 3 0 0
KpnI GGTACC 6 2 0 5 1 0 0
Ksp632I CTCTTC 6 2 0 7 10 0 0
MaeII ACGT 4 2 0 1 3 0 0
NotI GCGGCCGC 8 2 0 2 6 0 0
TaqI TCGA 4 2 0 1 3 0 0
File: REBASE/embossre.equ
Bsc4I BsiYI
Bse1I BsrI
BshI HaeIII
BsiSI HpaII
Bsu6I Ksp632I
HpyCH4IV MaeII
File: REBASE/embossre.ref
# REBASE enzyme information for EMBOSS
#
# Format:
# Line 1: Name of Enzyme
# Line 2: Organism
# Line 3: Isoschizomers
# Line 4: Methylation
# Line 5: Source
# Line 6: Suppliers
# Line 7: Number of following references
# Lines 8..n: References
# // (end of entry marker)
#
AaeI
Acetobacter aceti sub. liquefaciens
BamHI,AacI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II
,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,
Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902
I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,Gse
III,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,Rh
sI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba
1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,U
ba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I
,Uba1402I,Uba1414I
M. Van Montagu
1
Seurinck, J., van Montagu, M., Unpublished observations.
//
AciI
Arthrobacter citreus
?(5),-2(5)
NEB 577
N
2
Lunnen, K.D., Heiter, D., Wilson, G.G., Unpublished observations.
Polisson, C., Morgan, R.D., (1990) Nucleic Acids Res., vol. 18, pp. 5911.
//
AclI
Acinetobacter calcoaceticus M4
Psp1406I
3(5)
S.K. Degtyarev
IN
2
Degtyarev, S.K., Abdurashitov, M.A., Kolyhalov, A.A., Rechkunova, N.I., (1992)
Nucleic Acids Res., vol. 20, pp. 3787.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
//
BamHI
Bacillus amyloliquefaciens H
AacI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,
BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,B
sp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I
,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseI
II,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,Rhs
I,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1
163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Ub
a1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,
Uba1402I,Uba1414I
5(4)
ATCC 49763
ABCDEFGHIJKLMNOQRSTUV
10
Brooks, J.E., Howard, K.A., US Patent Office, 1994.
[Part of this file has been deleted for brevity]
ATCC 49790
ABCDEFGHIJKLMNOQRSTU
3
Kiss, A., Finta, C., Venetianer, P., (1991) Nucleic Acids Res., vol. 19, pp. 34
60.
Smith, D.I., Blattner, F.R., Davies, J., (1976) Nucleic Acids Res., vol. 3, pp.
343-353.
Tomassini, J., Roychoudhury, R., Wu, R., Roberts, R.J., (1978) Nucleic Acids Re
s., vol. 5, pp. 4055-4064.
//
Ksp632I
Kluyvera species 632
Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,T
deII,Uba1192I,Uba1276I,VpaKutEI,VpaKutFI,VpaO5I
DSM 4196
M
2
Bolton, B.J., Schmitz, G.G., Jarsch, M., Comer, M.J., Kessler, C., (1988) Gene,
vol. 66, pp. 31-43.
Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides & Nucleo
tides, vol. 13, pp. 1617-1626.
//
MaeII
Methanococcus aeolicus PL-15/H
HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI
K.O. Stetter
M
1
Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O., Sch
mitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.
//
NotI
Nocardia otitidis-caviarum
CciNI,CspBI,MchAI
?(4)
ATCC 14630
ABCDEFGHJKLMNOQRSTU
4
Borsetti, R., Wise, D., Qiang, B.-Q., Schildkraut, I., Unpublished observations
.
Morgan, R.D., Unpublished observations.
Morgan, R.D., Benner, J.S., Claus, T.E., US Patent Office, 1994.
Qiang, B.-Q., Schildkraut, I., (1987) Methods Enzymol., vol. 155, pp. 15-21.
//
TaqI
Thermus aquaticus YTI
CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30
I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,
HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok
4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,
TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
4(6)
J.I. Harris
ABCDEFGIJLMNOQRSTU
5
Anton, B.P., Brooks, J.E., Unpublished observations.
Fomenkov, A., Xiao, J.-P., Dila, D., Raleigh, E., Xu, S.-Y., (1994) Nucleic Aci
ds Res., vol. 22, pp. 2399-2403.
McClelland, M., (1981) Nucleic Acids Res., vol. 9, pp. 6795-6804.
Sato, S., Hutchison, C.A. III, Harris, J.I., (1977) Proc. Natl. Acad. Sci. U. S
. A., vol. 74, pp. 542-546.
Zebala, J.A., (1993) Diss. Abstr., vol. 54, pp. 1394-1398.
//
File: REBASE/embossre.sup
# REBASE Supplier information for EMBOSS
#
# Format:
# Code of Supplier<ws>Supplier name
#
A Amersham Pharmacia Biotech (1/01)
B Life Technologies Inc. (1/98)
C Minotech, Molecular Biology Products (12/00)
D HYBAID GmbH (12/00)
E Stratagene (11/00)
F Fermentas AB (5/01)
G Q-BIOgene (1/01)
H American Allied Biochemical, Inc. (10/98)
I SibEnzyme Ltd. (1/01)
J Nippon Gene Co., Ltd. (6/00)
K Takara Shuzo Co. Ltd. (2/01)
L Transgenomic Ltd. (1/01)
M Roche Molecular Biochemicals (1/01)
N New England BioLabs (12/00)
O Toyobo Biochemicals (11/98)
P Megabase Research Products (5/99)
Q CHIMERx (10/97)
R Promega Corporation (6/99)
S Sigma Chemical Corporation (11/98)
T Advanced Biotechnologies Ltd. (3/98)
U Bangalore Genei (2/01)
V MRC-Holland (3/01)
The output files are held in the REBASE subdirectory of the EMBOSS
data directory. There are three:
* embossre.enz Enzyme pattern file
* embossre.ref Enzyme references
* embossre.sup Enzyme suppliers
rebaseextract will also (by default) produce an 'embossre.equ' file in
the EMBOSS data directory. This can be turned off by setting the
-equivalences option to be false. This option calculates an
'embossre.equ' file using restriction enzyme prototypes in the
"withrefm" file. The 'embossre.equ' file is a file of preferred
isoschizomers. You may edit it to contain your available restriction
enzymes.
Data files
The "withrefm" file of an REBASE distribution is the input file for
this program.
Notes
The home page of REBASE is: http://rebase.neb.com/
Running this program may be the job of your system manager.
The ready-made files produced by this program may already be available
at the REBASE web site: http://rebase.neb.com/rebase/rebase.files.html
or http://rebase.neb.com/rebase/rebase.f37.html
References
1. Nucleic Acids Research 27: 312-313 (1999).
Warnings
The program will warn you if the input file is incorrectly formatted.
Diagnostic Error Messages
Exit status
It exits with status 0 unless an error is reported.
Known bugs
See also
Program name Description
aaindexextract Extract data from AAINDEX
cutgextract Extract data from CUTG
printsextract Extract data from PRINTS
prosextract Build the PROSITE motif database for use by patmatmotifs
tfextract Extract data from TRANSFAC
Author(s)
Alan Bleasby (ajb ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
History
Completed 12th April 1999
Target users
This program is intended to be used by administrators responsible for
software and database installation and maintenance.
Comments
None
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