| 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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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
    Full pathname of WITHREFM file: ../../data/withrefm
    Full pathname of PROTO file: ../../data/proto

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-inf]               infile     Full pathname of WITHREFM file
      [-proto]             infile     Full pathname of PROTO file

       Optional qualifiers:
       -[no]equivalences   boolean    This option calculates an embossre.equ file
                                      using restriction enzyme prototypes in the
                                      withrefm file.

       Advanced 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-inf] (Parameter 1) | Full pathname of WITHREFM file | Input file | Required
[-proto] (Parameter 2) | Full pathname of PROTO file | Input file | Required
Optional qualifiers | Allowed values | Default
-[no]equivalences | This option calculates an embossre.equ file using restriction enzyme prototypes in the withrefm file. | Boolean value Yes/No | Yes
Advanced qualifiers | Allowed values | Default
(none)

## 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: ../../data/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]

    <6>S.A. Thompson
    <7>N
    <8>Morgan, R.D., Unpublished observations.
    Morgan, R.D., Xu, Q., US Patent Office, 2001.
    Xu, Q., Morgan, R., Blaser, M., Unpublished observations.

    <1>HspAI
    <2>HhaI,AspLEI,BcaI,BspLAI,BstHHI,CcoP95I,CfoI,Csp1470I,FnuDIII,Hin6I,Hin7I,HinGUI,HinP1I,HinS1I,HinS2I,Hpy99III,HpyF10I,HsoI,MnnIV,NgoEII,SciNI
    <3>G^CGC
    <4>
    <5>Haemophilus species A
    <6>S.K. Degtyarev
    <7>I
    <8>Rechkunova, N.I., Prikhod'ko, E.A., Shevchenko, A.V., Degtyarev, S.K., Unpublished observations.

    <1>KpnI
    <2>Acc65I,AhaB8I,Asp718I,BspJ106I,Eco149I,Esp19I,KpnK14I,MvsI,MvsAI,MvsBI,MvsCI,MvsDI,MvsEI,NmiI,Sau10I,SthI,SthAI,SthBI,SthCI,SthDI,SthEI,SthFI,SthGI,SthHI,SthJI,SthKI,SthLI,SthMI,SthNI,Uba76I,Uba85I,Uba86I,Uba87I,Uba1201I
    <3>GGTAC^C
    <4>4(6)
    <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>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: ../../data/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
    	    ---------------

    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

### File: REBASE

### File: embossre.equ

    Bsc4I BsiYI
    Bse1I BsrI
    BshI HaeIII
    BsiSI HpaII
    Bsu6I Ksp632I
    HpyCH4IV MaeII

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 | Builds the PROSITE motif database for patmatmotifs to search
tfextract | Extract data from TRANSFAC

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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