
                               rebaseextract 



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

   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. 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 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 from CUTG database
   jaspextract Extract data from JASPAR
   printsextract Extract data from PRINTS database for use by pscan
   prosextract Processes the PROSITE motif database for use by
   patmatmotifs
   tfextract Process TRANSFAC transcription factor database for use by
   tfscan

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
