restriction enzyme database (REBASE)

Dr. Richard Roberts at Cold Spring Harbor Laboratory roberts at CSHL.ORG
Thu Dec 12 16:35:44 EST 1991


!Date: Wed, 11 Dec 91 9:29:57 EST
!X-Mailer: ELM [version 2.3 PL11]
!Status: RO
!
!	Can anyone advise me on how to gain access to the databank
!on restriction enzymes?  I only have a dumb terminal, so WAIS is out
!of the question.  I tried SWAIS but had no luck.  I also tried Archie
!and there seems to be something in an FTP site in Japan, but the
!path which Archie described didn't want to work when I tried to get
!it via FTP.  Thanks for any replies.

!Mike Coady
!COADY at ERE.UMONTREAL.CA

!* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

The original files from REBASE are described below and can be obtained by e-mail
or by anonymous ftp


REBASE OPTIONS:




             Copyright (c) Cold Spring Harbor Laboratory 1991
       		           All rights reserved.




                   RESTRICTION ENZYME DATABASE (REBASE)




The Restriction Enzyme Database, REBASE, is a repository of information 
about the known restriction enzymes, methylases, and the microorganisms 
from which they have been isolated.  Documents (from 1952-present) that 
describe the isolation of an enzyme or contribute observations relating 
to an enzyme's properties are logged in REBASE, along with other useful 
information, such as the commercial availability of the enzymes.


			--------------------------

   REBASE updates (ASCII flat files) are distributed electronically, at 
monthly intervals and at no charge.  These are available in many output 
formats.  Other formats can be provided upon request.  We are prepared 
to support each major sequence analysis package.

For those of you on the internet, an anonymous FTP site is now available. 
The command "ftp rna.cshl.org" will get you in.  In response to user name 
just type "anonymous" or "ftp". Our REBASE files can then be found in the 
directory pub/rebase.  All of the files that we distribute electronically 
will be kept there, along with any other related information.

			--------------------------

	CURRENTLY AVAILABLE FORMATS:

	1.  All Type II with separate reference list
	2.  All Types I, II & III (with separate reference list)
	3.  All Types I, II & III (individually referenced)
	4.  NAR (see Nucleic Acids Research 19: 2077-2109, 1991)
	5.  A list of all prototypes
	6.  UWGCG data file
	7.  IG Suite data file
	8.  ALPHAZYMES - for CSHL software
	9.  CUTZYMES - for CSHL software
       10.  Staden data file
       11.  Mac Report - a listing of all references, with abstracts
       12.  IBM Report - a listing of all references, with abstracts
       13.  DNA Strider data file
       14.  UWGCG data file - with reference list
       15.  Type II (with tabs)
       16.  Type II (with isoschizomers)
       17.  Commercial Restriction Enzyme Listing
       18.  Commercial Address List
       19.  DNA Strider data file (commercially available enzymes only)
       20.  Commercial Restriction Enzyme Info
       21.  All Types I, II & III (parsed references)  
       22.  All Types I, II & III (sorted by microorg)  
       23.  Commercial Methylase Listing
       24.  Commercial Methylase Info  

			--------------------------
CONTACT:

	For more information or to be placed on the mailing list

		write:  Dr. Richard J. Roberts
			Cold Spring Harbor Laboratory
			Cold Spring Harbor, New York 11724-2202  U.S.A.

		phone:	(516) 367-8388
		fax:	(516) 367-8461
		email:	roberts at cshl.org



	(Be sure to include an email address, postal address with 
	full name, telephone number, and FAX number, if available.)


----------------------------------------------------------------------------
1.                       ---   Type II format   ---
----------------------------------------------------------------------------
DESCRIPTION:    a list of type II enzymes and a list of their associated 
                references. 


EXAMPLE of Type II enzyme list:


<1><name>
<2><prototype>
<3><recognition sequence>
<4><methylation site>
<5><commercial source>
<6><references>

<1>AluI
<2>
<3>AG^CT
<4>3(5)
<5>ABDEFGHIJKLMNOPQRSUVX
<6>320,507,700,701

<1>AlwI
<2>BinI
<3>GGATC(4/5)
<4>
<5>NU
<6>404
                      -------------------------------

EXAMPLE of reference list:

1.	Agarwal, K. unpublished observations.
2.	Aiken, C., Milarski-Brown, K., Gumport, R.I. (1986) Fed. Proc. 
	45: 1914
3.	Akulinin, G.E., Getko, G.A., Repin, V.E., Degtyarev, S.K. (1988) 
	Izv Sib Otd Akad. Nauk SSSR Ser Biol Nauk 14: 105-108
4.	Arrand, J.R., Myers, P.A., Roberts, R.J. (1978) J. Mol. Biol. 
	118: 127-135
5.	Arrand, J.R., Myers, P.A., Roberts, R.J. unpublished 
	observations.
6.	Arutyunyan, E.E., Gruber, I.M., Polyachenko, V.M., Kvachadze, 
	L.J., Andriashvili, I.A., Chanishvili, T.G., Nikolskaya, I.I. (1985) 
	Vopr. Med. Khim. 31: 127-132
7.	Aubert, E., Davies, J., Williams, R. unpublished observations.

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
2.                 ---   ALL ENZYMES (REFERENCE LIST)   ---
-------------------------------------------------------------------------------
DESCRIPTION:
               A list of all restriction enzymes - Types I, II, and III. 
               References are numbered and listed seperately at the bottom 
               of the report.

EXAMPLE:


<1>ENZYME NAME: self explanatory
<2>PROTOTYPE: The name of the first enzyme discovered with this specificity.
<3>MICROORGANISM: self explanatory
<4>SOURCE: Either an individual or a National Culture Collection.
<5>RECOGNITION SEQUENCE: These are written from 5' to 3', only one strand being
given, and the point of cleavage is indicated ^.  When no ^ appears, the
precise cleavage site has not been determined.  For enzymes such as HgaI,
MboII etc., which cleave away from their recognition sequence the sites of
cleavage are indicated in parentheses.  For example HgaI GACGC (5/10)
indicates cleavage as shown below
5' GACGCNNNNN^      3'
3' CTGCGNNNNNNNNNN^ 5'
In all cases the recognition sequences are oriented so that the cleavage sites
lie on their 3' side.
Recognition sequences are given using 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
<6>METHYLATION SITE: The site of methylation by the cognate methylase when known
is indicated as follows.  The first number shows the base within the
recognition sequence that is modified.  A negative number indicates the
complementary strand, numbered from the 5' base of that strand.  The number in
parentheses indicates the specific methylation involved. (6) = N6-
methyladenosine (5) = 5-methylcytosine (4) = N4-methylcytosine.
<8>COMMERCIAL AVAILABILITY: commercial abbreviations as assigned in REBASE
<9>REFERENCES: only the primary references for the isolation and/or purification
of the restriction enzyme or methylase, the determination of the recognition
sequence and cleavage site or the methylation specificity are given.

<1>AaaI
<2>XmaIII
<3>Acetobacter aceti ss aceti
<4>M. Fukaya
<5>C^GGCCG
<6>
<7>
<8>600

<1>AacI
<2>BamHI
<3>Acetobacter aceti sub. liquefaciens
<4>IFO 12388
<5>GGATCC
<6>
<7>
<8>532

<1>AaeI
<2>BamHI
<3>Acetobacter aceti sub. liquefaciens
<4>M. Van Montagu
<5>GGATCC
<6>
<7>
<8>532

------------------------------------------------------------------------------
------------------------------------------------------------------------------
3.               ---   ALL ENZYMES (INDIVIDUALLY REFERENCED)  ---
------------------------------------------------------------------------------
DESCRIPTION:    a list of all restriction enzymes - Types I, II, and III.
                Similar to above format except that instead of including
                the references at the bottom of the report, each enzyme
                is followed by its reference information.

EXAMPLE:


<ENZYME NAME>self explanatory
<PROTOTYPE>The name of the first enzyme discovered with this specificity.
<MICROORGANISM>self explanatory
<SOURCE>Either an individual or a National Culture Collection.
<RECOGNITION SEQUENCE>These are written from 5' to 3', only one strand being
given, and the point of cleavage is indicated ^.  When no ^ appears, the
precise cleavage site has not been determined.  For enzymes such as HgaI,
MboII etc., which cleave away from their recognition sequence the sites of
cleavage are indicated in parentheses.  For example HgaI GACGC (5/10)
indicates cleavage as shown below
5' GACGCNNNNN^      3'
3' CTGCGNNNNNNNNNN^ 5'
In all cases the recognition sequences are oriented so that the cleavage sites
lie on their 3' side.
Recognition sequences are given using 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
<METHYLATION SITE>The site of methylation by the cognate methylase when known
is indicated as follows.  The first number shows the base within the
recognition sequence that is modified.  A negative number indicates the
complementary strand, numbered from the 5' base of that strand.  The number in
parentheses indicates the specific methylation involved. (6) = N6-
methyladenosine (5) = 5-methylcytosine (4) = N4-methylcytosine.
<COMMERCIAL AVAILABILITY>commercial abbreviations as assigned in REBASE
<REFERENCES>only the primary references for the isolation and/or purification
of the restriction enzyme or methylase, the determination of the recognition
sequence and cleavage site or the methylation specificity are given.

<1>AaaI
<2>XmaIII
<3>Acetobacter aceti ss aceti
<4>M. Fukaya
<5>C^GGCCG
<6>
<7>
<8>Tagami, H., Tayama, K., Tohyama, T., Fukaya, M., Okumura, H., Kawamura, Y., 
   Horinouchi, S., Beppu, T. Purification and properties of a site-specific 
   restriction endonuclease AaaI from Acetobacter aceti subsp. aceti No. 1023.
   FEMS Microbiol. Lett. 56: 161-166 (1988)

<1>AacI
<2>BamHI
<3>Acetobacter aceti sub. liquefaciens
<4>IFO 12388
<5>GGATCC
<6>
<7>
<8>Seurinck, J., van Montagu, M. unpublished observations.

<1>AaeI
<2>BamHI
<3>Acetobacter aceti sub. liquefaciens
<4>M. Van Montagu
<5>GGATCC
<6>
<7>
<8>Seurinck, J., van Montagu, M. unpublished observations



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