rebaseextract
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Function
Process the REBASE database for use by restriction enzyme applications
Description
rebaseextract processes the REBASE database for use by the EMBOSS
restriction enzyme applications. It 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 of preferred
isoschizomers using restriction enzyme prototypes in the "proto" file.
This can be turned off by setting the -equivalences option to be false.
Usage
Here is a sample session with rebaseextract
% rebaseextract
Process the REBASE database for use by restriction enzyme applications
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
Process the REBASE database for use by restriction enzyme applications
Version: EMBOSS:6.6.0.0
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 first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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
-version boolean Report version number and exit
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 Res
., vol. 5, pp. 4055-4064.
<1>Ksp632I
<2>Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI
,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) Gen
e, vol. 66, pp. 31-43.
Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides & Nucleot
ides, 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., S
chmitt, 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 observatio
ns.
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,HpyF
30I,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,T
spAK16D24I,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 Acid
s 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,Bs
p98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,B
stQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,
MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rl
u4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,
Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I
,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,Uba1402
I,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) N
ucleic 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,B
amFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,Bsp
98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,Bs
tQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,M
leI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu
4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,U
ba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,
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. 346
0.
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 Res
., vol. 5, pp. 4055-4064.
//
Ksp632I
Kluyvera species 632
Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,Td
eII,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 & Nucleot
ides, 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., Schm
itt, 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,HpyF30I
,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,Hp
yF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2
I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,TspA
K16D24I,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 Acid
s 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 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/
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.
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
You may edit the embossre.equ file it to contain details for your
available restriction enzymes.
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 amino acid property data from AAINDEX
cutgextract Extract codon usage tables from CUTG database
jaspextract Extract data from JASPAR
printsextract Extract data from PRINTS database for use by pscan
prosextract Process the PROSITE motif database for use by patmatmotifs
tfextract Process TRANSFAC transcription factor database for use by
tfscan
Author(s)
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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