
                               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   contains published and unpublished references, recognition and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.
   
   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: ../../data/withrefm
   
   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

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-inf]
   (Parameter 1) Full pathname of WITHREFM Input file Required
   Optional qualifiers Allowed values Default
   (none)
   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,Hin
GUI,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., Unpub
lished 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,S
thJI,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 Re
s., 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 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.
   
Output file format

  Output files for usage example
  
  File: REBASE
  
   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
       
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)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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
