EMBOSS: rebaseextract

| rebaseextract

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## 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:6.5.6.0

       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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-infile] (Parameter 1) | infile | REBASE database withrefm file | Input file | Required
[-protofile] (Parameter 2) | infile | REBASE database proto file | Input file | Required
Additional (Optional) qualifiers
-[no]equivalences | boolean | This option calculates an embossre.equ file using restriction enzyme prototypes in the withrefm file. | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
(none)
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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) Gene, vol. 66, pp. 31-43.
    Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides & Nucleotides, 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 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.

    <1>TaqI
    <2>CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,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 Acids 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,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,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,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,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,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,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. 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.
    //
    Ksp632I
    Kluyvera species 632
    Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,TdeII,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 & Nucleotides, 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., Schmitt, 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,HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok4A2I,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 Acids 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 © 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