=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= REBASE, The Restriction Enzyme Database http://rebase.neb.com Copyright (c) Dr. Richard J. Roberts, 2004. All rights reserved. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= R E B A S E The Restriction Enzyme Database 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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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. REBASE is updated daily. Each month, a set of REBASE datafiles are released publically and distributed to the scientific community at no charge via a regular monthly emailing list, and made available via ftp (ftp://ftp.neb.com) and the web (http://rebase.neb.com). Many of these data files have been designed specifically for use with a variety of software packages, such as GCG, DNA Strider, and IntelliGenetics. As REBASE expands, an ever-growing number of new data files are being provided. Requests for additional formats are welcome, as we are prepared to support each major sequence analysis package. Dr. Richard J. Roberts New England BioLabs 32 Tozer Road Beverly, Massachusetts 01915 U.S.A. phone: (978) 927-5054 fax: (978) 921-1527 email: roberts@neb.com Latest Review: Nucleic Acids Research 31: 418-420 (2003). ****************************************************************************** RECOGNITION SEQUENCE NOMENCLATURE 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. Bsp24I 5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3' 3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5' This will be described in some REBASE reports as: Bsp24I (8/13)GACNNNNNNTGG(12/7) COMMERCIAL AVAILABILITY Each commercial source of restriction enzymes and/or methylases listed in REBASE is assigned a single character abbreviation code. For example: F Fermentas AB (12/02) N New England Biolabs (1/03) The date in parentheses indicates the most recent update of that organization's listings in REBASE. ****************************************************************************** REBASE via ANONYMOUS FTP: ftp ftp.neb.com (username: anonymous, password: your email address) cd pub/rebase (to enter the correct directory) dir (to list the names of available files) get Readme |more (to view the file called Readme, spaces matter!) get Readme (to copy the file called Readme to your machine) quit (returns you back to your local system) ****************************************************************************** REBASE via EMAIL: To be placed on our monthly emailing list, send your full name, postal address, telephone number, fax number (if available), and email address to macelis@neb.com ****************************************************************************** CURRENT EMAILING LIST FILES to get (### = current version & FTP SITE FORMATS ex. 302 indicates February 2003) #1. COMMERCIAL SOURCES commdata.### #2. GCG (also SEQTools,GeneDoc, and BioEdit) gcg.### #3. GCG (with refs) gcgenz.###, gcgref.### #4. Nucleic Acids Research nar.### #5. Prototypes proto.### #6. Type II (Oligo,Primer/SimVector) type2.###, type2ref.### #7. Type II (with isos) gtype2.###, type2ref.### #8. Type II (tabbed output) itype2.###, type2ref.### #9. All Enzymes (ref list) (Redasoft Plasmid) allenz.### #10. All Enzymes (each w/ ref) withref.### #11. All Enzymes (parsed refs) parsrefs.### #12. All Enzymes (by microorg) orgref.### #13. IGSuite bionet.### #14. ALPHAZYMES azymes.### #15. CUTZYMES cutzymes.### #16. STADEN staden.### #17. DNA Strider, DNAssist, strider.### and Sequence Quickie-Calc #18. DNA Strider (commercial enzymes), striderc.### DNAssist, and Sequence Quickie-Calc #19. MacVector, Vector NTI, PC/Gene (Bairoch) bairoch.doc, bairoch.### #20. DNASIS dnasis.### #21. PUBLISHED REFS pubrefs.###, pubrefsa.### #22. Pro-Cite / EndNote Refs procite.###, procitea.### #23. GENEPRO genepro.### #24. GENEPRO (commercial) geneproc.### #25. REBASE NEWS (release notes) NEWS.### #26. Prototypes and Neoschizomers neos.### #27. Reference Manager refmgr.### #28. SEQAIDII seqaidii.### #29. GENETYX genetyx.### #30. IGSuite (commercial) bionetc.### #31. All Enzymes (each w/ ref & isos) withrefm.### #32. Type II (with isos) (commercial) gtype2c.###, type2ref.### #33. CAD Gene cadgene.### #34. Homing Endonucleases homing.### #35. Clone Manager clonemgr.### #36. Gene Runner generunr.### #37. EMBOSS emboss_e.###, emboss_r.### emboss_s.### #38. Bairoch-Mini (commercial type II RE) bairochc.###, bairoch.doc Information about OTHER DATA FORMATS - at the end of this document (DNAStar, Gene Construction Kit, Gene Inspector, Sequencher...) ********************************** DESCRIPTIONS OF AVAILABLE FORMATS: ********************************** ****************************************************************************** #1. COMPLETE COMMERCIAL SOURCE INFORMATION GET FILE(S): commdata.### DESCRIPTION: commmercial suppliers of restriction enzymes and methylases. Includes contact information: postal & email addresses, telephone/fax #'s, web sites, distributors, REBASE codes for each company and the names of the enzymes that they sell. ****************************************************************************** #2. GCG FORMAT GET FILE(S): gcg.### DESCRIPTION: format used as input for the Sequence Analysis Software Package by Genetics Computer Group. Also usable with SEQTools, GeneDoc and BioEdit. EXAMPLE: enzyme name cut site rec seq w cut sites marked overhang commer abbrs .. ;AatI 3 AGG'CCT 0 ! StuI,Eco147I >OU AatII 5 G_ACGT'C -4 ! >EGMNOPRSUVX AccI 2 GT'mk_AC 2 ! >ABEGIKMNOPRSUVX ;AccII 2 CG'CG 0 ! ThaI,BstUI,MvnI,Bsp50I >AEGKVX ;AccIII 1 T'CCGG_A 4 ! BspMII,Kpn2I,MroI >AEGKR AgeI 1 A'CCGG_T 4 ! > AluI 2 AG'CT 0 ! >ABEFGIKMNOPRSUVX ****************************************************************************** #3. GCG - with refs GET FILE(S): gcgenz.###, gcgref.### DESCRIPTION: two files: the first can be used as input for the Sequence Analysis Software Package by Genetics Computer Group;the 2nd contains a reference list for all enzymes named in the first file (where the final column in an enzyme entry contains the number for the related references). Same as format #2, except reference information is given. EXAMPLE of enzyme file: enzyme name cut site rec seq w cut sites marked overhang commer refs .. ;AatI 3 AGG'CCT 0 ! StuI,Eco147I >OU 2 AatII 5 G_ACGT'C -4 ! >EGJLMNOPRSUVX 2 AccI 2 GT'mk_AC 2 ! >ABDEGIJKLMNOPQRSUVX 3 ;AccII 2 CG'CG 0 ! FnuDII,ThaI,BstUI,MvnI,Bsp50I >ADEGJKQVX 1,3 EXAMPLE of reference file: References: 1. Kita, K., Hiraoka, N., Kimizuka, F., Obayashi, A. (1984) Agric. Biol. Chem. 48: 531-532 2. Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M. (1982) Nucl. Acids Res. 10: 5747-5752 3. Zabeau, M., Roberts, R.J. unpublished observations. ****************************************************************************** #4. NAR format GET FILE(S): nar.### DESCRIPTION: a list of Type II, I and III enzymes in a format close to that used in our Nucleic Acids Research Supplement reviews. Included in this list are all prototypes, their neoschizomers, and commercially available isoschizomers. EXAMPLE: prototype rec seq w cut site methylation site, type commer refs isoschizomer rec seq w cut site methylation site, type commer refs AatII GACGT^C EJLMNO 6 AciI CCGC(-3/-1) N 3 AhaIII TTT^AAA 8 DraI TTT^AAA KLMNO 4 ApaI GGGCC^C 4(5) KLMNOX 5,7 Bsp120I G^GGCCC F 1,2 References: 1. Janulaitis, A.A., Gilvonauskaite, R., Petrusyte, M. unpublished observations. 2. Janulaitis, A.A., Maneliene, Z., Butkus, V. unpublished observations. 3. Polisson, C., Morgan, R.D. (1990) Nucl. Acids Res. 18: 5911 4. Purvis, I.J., Moseley, B.E.B. (1983) Nucl. Acids Res. 11: 5467-5474 5. Seurinck, J., Van de Voorde, A., Van Montagu, M. (1983) Nucl. Acids Res. 11: 4409-4415 6. Sugisaki, H., Maekawa, Y., Kanazawa, S., Takanami, M. (1982) Nucl. Acids Res. 10: 5747-5752 7. Trautner, T.A. unpublished observations. 8. Whitehead, P.R., Brown, N.L. (1982) FEBS Lett. 143: 296-300 ****************************************************************************** #5. PROTOTYPES GET FILE(S): proto.### DESCRIPTION: a list of all prototypes and their recognition sequences. EXAMPLE: enzyme name recognition sequence with cleavage site AatII GACGT^C AccI GT^MKAC AcyI GR^CGYC AflII C^TTAAG AflIII A^CRYGT ****************************************************************************** #6. Type II format GET FILE(S): type2.###, type2ref.### DESCRIPTION: two files: a list of type II restriction enzymes, and a list of their associated references. This format is used by Molecular Biology Insights' OLIGO Primer Analysis Software and by PREMIER Biosoft International's Primer Premier and SimVector EXAMPLE of Type II enzyme list: <1>enzyme name <2>prototype <3>recognition sequence with cleavage site <4>methylation site and type <5>commercial source <6>references <1>ApaI <2> <3>GGGCC^C <4>4(5) <5>BDEIJKLMNOPRSUVXY <6>2,3 <1>Zsp2I <2>AvaIII <3>ATGCA^T <4> <5>DY <6>1 EXAMPLE of reference list: 1. Degtyarev, S.K. unpublished observations. 2. Seurinck, J., Van de Voorde, A., Van Montagu, M. (1983) Nucl. Acids Res. 11: 4409-4415. 3. Trautner, T.A. unpublished observations. ****************************************************************************** #7. Type II with Isoschizomers GET FILE(S): gtype2.### (LARGE file. 1MB+), type2ref.### DESCRIPTION: a list of type II enzymes and a list of their associated references. Same as format #6, except that instead of just the prototype in field 2, all isoschizomers are listed. Separate reference file, as in format #6. EXAMPLE: <1>enzyme name <2>isoschizomers <3>recognition sequence with cleavage site <4>methylation site and type <5>commercial source <6>references <1>AluI <2>BsaLI,MltI,OtuI,OtuNI,OxaI <3>AG^CT <4>3(5) <5>ABDEFGHIJKLMNOPQRSUVX <6>320,507,700,701 <1>AlwI <2>BinI,BthII <3>GGATC(4/5) <4> <5>NU <6>404 ****************************************************************************** #8. Type II format with tabs GET FILE(S): itype2.###, type2ref.### DESCRIPTION: a list of type II enzymes and a list of their associated references. Same as format #6, except that the fields are separated by tabs, so that each enzyme entry is on a single line. Separate reference file, as in format #6. EXAMPLE of Type II enzyme list: tab tab tab tab tab AluI AG^CT 3(5) ABDEFGHIJKLMNOPQRSUVX 320,507,700,701 AlwI BinI GGATC(4/5) NU 404 Alw21I HgiAI GWGCW^C DF 226 Alw26I BsmAI GTCTC(1/5) DFR 161 Alw44I ApaLI G^TGCAC DFORU 226 AlwNI CAGNNN^CTG NU 407 ****************************************************************************** #9. ALL ENZYMES (REFERENCE LIST) GET FILE(S): allenz.### DESCRIPTION: A list of all restriction enzymes - Types I, II, and III. References are numbered and listed separately at the bottom of the report. This format is used by Redasoft Plasmid. EXAMPLE: <1>enzyme name <2>prototype <3>microorganism <4>source of microorganism <5>recognition sequence with cleavage site <6>methylation site and type <7>commercial source <8>references <1>AluI <2> <3>Arthrobacter luteus <4>ATCC 21606 <5>AG^CT <6>3(5) <7>ABEFHIJKLMNOPQRSUVX <8>1,3,4,5 <1>AlwI <2>BinI <3>Acinetobacter lwoffi <4>NEB 402 <5>GGATC(4/5) <6> <7>NSU <8>2 References: 1. Kramarov, V.M., Smolyaninov, V.V. (1981) Biokhimiya 46: 1526-1529 2. Morgan, R., Bonventre, J. unpublished observations. 3. Roberts, R.J., Myers, P.A., Morrison, A., Murray, K. (1976) J. Mol. Biol. 102: 157-165 4. Yoon, H., Suh, H., Han, M.H., Yoo, O.J. (1985) Korean Biochem. J. 18: 82-87 5. Yoon, H., Suh, H., Kim, K., Han, M.H., Yoo, O.J. (1985) Korean Biochem. J. 18: 88-93 ****************************************************************************** #10. ALL ENZYMES (INDIVIDUALLY REFERENCED) GET FILE(S): withref.### DESCRIPTION: a list of all restriction enzymes - Types I, II, and III. Similar to format #9 except that instead of including the references at the bottom of the report, each enzyme is followed by its reference information. EXAMPLE: <1>enzyme name <2>prototype <3>microorganism <4>source of microorganism <5>recognition sequence with cleavage site <6>methylation site and type <7>commercial source <8>references <1>AluI <2> <3>Arthrobacter luteus <4>ATCC 21606 <5>AG^CT <6>3(5) <7>ABEFHIJKLMNOPQRSUVX <8>Kramarov, V.M., Smolyaninov, V.V. DNA methylase from Arthrobacter luteus screens DNA from the action of site-specific endonuclease AluI. Biokhimiya 46: 1526-1529 (1981) Roberts, R.J., Myers, P.A., Morrison, A., Murray, K. A specific endonuclease from Arthrobacter luteus. J. Mol. Biol. 102: 157-165 (1976) Yoon, H., Suh, H., Han, M.H., Yoo, O.J. Purification and characterization of AluI methylase. Korean Biochem. J. 18: 82-87 (1985) Yoon, H., Suh, H., Kim, K., Han, M.H., Yoo, O.J. The specificity & catalytic properties of AluI methylase. Korean Biochem. J. 18: 88-93 (1985) <1>ApaI <2> <3>Acetobacter pasteurianus sub. pasteurianus <4>NCIB 7215 <5>GGGCC^C <6>4(5) <7>BEIJKLMNOPRSUVX <8>Seurinck, J., Van de Voorde, A., Van Montagu, M. A new restriction endonuclease from Acetobacter pasteurianus. Nucl. Acids Res. 11: 4409-4415 (1983) Trautner, T.A. unpublished observations. ****************************************************************************** #11. ALL ENZYMES (PARSED REFERENCES) GET FILE(S): parsrefs.### DESCRIPTION: A list of all restriction enzymes - Types I, II, and III. In this report, references are listed in a parsed format. EXAMPLE: <1>enzyme name <2>prototype <3>microorganism <4>source of microorganism <5>recognition sequence with cleavage site <6>methylation site and type <7>commercial source <8>references <1>CviJI <2> <3>Chlorella strain NC64A (IL-3A) <4>J.L. Van Etten <5>RG^CY <6>3(5) <7> <8>1,603 <1>DdeI <2> <3>Desulfovibrio desulfuricans Norway strain <4>H. Peck <5>C^TNAG <6>1(5) <7>BEGIJLMNOPRUVX <8>177,232,397 References: 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 ****************************************************************************** #12. ALL ENZYMES (SORTED BY ORGANISM) GET FILE(S): orgref.### DESCRIPTION: This is a complete list of enzymes currently stored in the database. Each enzyme is followed by its reference information. The enzymes are sorted by their microorganism names. EXAMPLE: <1>enzyme name <2>prototype <3>microorganism <4>source of microorganism <5>recognition sequence with cleavage site <6>methylation site and type <7>commercial source <8>references <1>ApaI <2> <3>Acetobacter pasteurianus sub. pasteurianus <4>NCIB 7215 <5>GGGCC^C <6>4(5) <7>BDEGIJKLMNOPRUVX <8>Seurinck, J., Van de Voorde, A., Van Montagu, M. A new restriction endonuclease from Acetobacter pasteurianus. Nucl. Acids Res. 11: 4409-4415 (1983) Trautner, T.A. unpublished observations. ****************************************************************************** #13. IG Suite format GET FILE(S): bionet.### DESCRIPTION: an alphabetical listing of Type II restriction enzymes, their prototypes, and recognition sequences with cut sites indicated. EXAMPLE: enzyme name (prototype) recognition sequence AaaI (XmaIII) C^GGCCG AacI (BamHI) GGATCC AatI (StuI) AGG^CCT AatII GACGT^C AcaII (BamHI) GGATCC ****************************************************************************** #14. ALPHAZYMES FORMAT GET FILE(S): azymes.### DESCRIPTION: an alphabetical list of all prototypes and their isoschizomers. Each is followed by its recognition sequence and commercial sources. For use with the CSHL sequence analysis programs. EXAMPLE: prototype recognition sequence w cut site enzyme type commer isoschizomer recognition sequence w cut site commer AatII GACGT^C 2 G,M,N,O AccI GT^(A/C)(G/T)AC 2 M,N,S DsaVI GT(A/C)(G/T)AC AcyI GPu^CGPyC 2 M,R,U AhaII GPu^CGPyC N AosII GPu^CGPyC AstWI GPu^CGPyC AsuIII GPu^CGPyC BbiII GPu^CGPyC A,K HgiI GPu^CGPyC ****************************************************************************** #15. CUTZYMES FORMAT GET FILE(S): cutzymes.### DESCRIPTION: a list of all prototypes, their recognition sequences, cut sites, and enzyme type. For use with the CSHL sequence analysis programs. EXAMPLE: code enzyme name recognition sequence cut sites enzyme type C StySQI AACNNNNNNATACG 99 14 1 C StySQI AACNNNNNNATATG 99 14 1 C StySPI AACNNNNNNGTAC 99 13 1 C StySQI AACNNNNNNGTACG 99 14 1 C StySQI AACNNNNNNGTATG 99 14 1 C StySPI AACNNNNNNGTGC 99 13 1 C EcoKI AACNNNNNNGTGC 99 13 1 C HindIII AAGCTT 1 6 2 C SspI AATATT 3 6 2 ****************************************************************************** #16. STADEN FORMAT GET FILE(S): staden.### DESCRIPTION: a list of commercially available type II enzymes with known recognition sequences. Cuts are marked with an apostrophe. For use with Rodger Staden's software programs. EXAMPLE: enzyme name/recognition sequence with cleavage site// AatI/AGG'CCT// AatII/GACGT'C// AccI/GT'MKAC// AccII/CG'CG// AccIII/T'CCGGA// Alw26I/GTCTCN'NNNN/'NNNNNGAGAC// Alw44I/G'TGCAC// AlwI/GGATCNNNN'N/'NNNNNGATCC// BbvI/GCAGCNNNNNNNN'NNNN/'NNNNNNNNNNNNGCTGC// BcgI/GCANNNNNNTCGNNNNNNNNNNNN'/NN'NNNNNNNNNNCGANNNNNNTGC// BsmI/GAATGCN'/NG'CATTC// ****************************************************************************** #17. DNA STRIDER FORMAT GET FILE(S): strider.### DESCRIPTION: a list of all prototypes with known recognition sequences. Cut sites are marked with "/". "#" before the enzyme name indicates an asymmetrical cutter. Alternatively, see format #18, for ALL commercial enzymes. NOTES: To obtain DNA Strider, contact its author, Christian Marck (marck@jonas.saclay.cea.fr) Older versions are limited to about 180 entries per datafile, so to successfully import these files, delete your least favorite enzymes. The newest version of DNA Strider can import larger enzyme files. DNA Strider files are also compatible with: - DNAssist shareware (www.dnassist.com) and - The Sequence Quickie-Calc (www.molecularprogramming.com) EXAMPLE: enzyme name, recognition sequence with cleavage site, AatII, gacgt/c, #AciI, ccgc, 2, -2, AcyI, gr/cgyc, AhaIII, ttt/aaa, AluI, ag/ct, AlwNI, cagnnn/ctg, ApaBI, gcannnnn/tgc, ****************************************************************************** #18. DNA STRIDER FORMAT (commercial) GET FILE(S): striderc.### DESCRIPTION: Commercially available enzymes. Cut sites are marked with "/". "#" before the enzyme name indicates an asymmetrical cutter. Same as format #17, except that ALL commercially available enzymes are included. NOTES: To obtain DNA Strider, contact its author, Christian Marck (marck@jonas.saclay.cea.fr) Older versions are limited to about 180 entries per datafile, so to successfully import these files, delete your least favorite enzymes. The newest version of DNA Strider can import larger enzyme files. DNA Strider files are also compatible with: - DNAssist shareware (www.dnassist.com) and - The Sequence Quickie-Calc (www.molecularprogramming.com) EXAMPLE: enzyme name, recognition sequence with cleavage site, AatII, gacgt/c, #AciI, ccgc, 2, -2, AcyI, gr/cgyc, AhaIII, ttt/aaa, AluI, ag/ct, AlwNI, cagnnn/ctg, ApaBI, gcannnnn/tgc, ****************************************************************************** #19. Bairoch format (MacVector, Vector NTI, PC/Gene) GET FILE(S): bairoch.doc, bairoch.### (LARGE file. 1MB+-) DESCRIPTION: an alphabetical listing of all type I, II and III restriction enzymes and methylases, in a format that is compatible with PROSITE, SWISS-PROT, EMBL, ENZYME, ECD, EPD, HAEMB data banks. To import this file into MacVector, download Oxford Molecular's Group's free REBASE->MacVector utility: http://www.accelrys.com/products/macvector/rebase_converter.html Each enzyme record is organized as follows: ID enzyme name ET enzyme type AC REBASE accession number OS microorganism name PT prototype RS recognition sequence, cut site MS methylation site (type) CR commercial sources for the restriction enzyme CM commercial sources for the methylase RN [count] RA authors RL jour, vol, pages, year, etc. // DESCRIPTION OF FIELDS ID: restriction enzyme name (methylase name if no corresponding restriction enzyme with this acronym) ET: Rn (where n is the type of the restriction enzyme) M (indicates that there is a corresponding methylase) Rn* (indicates the restriction enzyme is of type n, but only recognizes the sequence when it is methylated.) AC: accession number assigned to this enzyme in REBASE OS: microorganism from which this enzyme is isolated PT: prototype of the enzyme RS: recognition sequence, cut site; [complementary strand rec seq, cut site;] MS: methylated base(type) [,methylated base(type) for complementary strand]; (where methylation type is: N4mC = N4-methylcytosine 5mC = 5-methylcytosine 6mA = 6-methyladenosine CR: REBASE single letter codes for the commercial sources of the restr. enzyme CM: REBASE single letter codes for the commercial sources of the methylase RN: [n] (where n shows the count of references given for this enzyme) RA: authors (lastname initials[, lastname initials]; RL: publication name volume:pages(year). (or Unpublished observations.) // (end-of-record marker) EXAMPLE: ID AluI ET R2 M AC RB30 OS Arthrobacter luteus PT AluI RS AGCT, 2; MS 3(5mC); CR A,B,E,F,H,I,K,L,M,N,O,P,Q,R,S,U,V,X. CM A,E,K,N,U. RN [1] RA Kramarov V.M., Smolyaninov V.V.; RL Biokhimiya 46:1526-1529(1981). RN [2] RA Roberts R.J., Myers P.A., Morrison A., Murray K.; RL J. Mol. Biol. 102:157-165(1976). RN [3] RA Yoon H., Suh H., Han M.H., Yoo O.J.; RL Korean Biochem. J. 18:82-87(1985). RN [4] RA Yoon H., Suh H., Kim K., Han M.H., Yoo O.J.; RL Korean Biochem. J. 18:88-93(1985). // ID M.BamHII ET M AC RB1218 OS Bacillus amyloliquefaciens H PT BamHII RS GGATCC, ?; MS 5; RN [1] RA Connaughton J.E., Vanek P.G., Chirikjian J.G.; RL J. Cell Biol. 107:535a-535a(1988). // ID CfuI ET R2* AC RB387 OS Caulobacter fusiformis BC-25 PT DpnI RS GATC, 2; RN [1] RA Butkus V., Padegimiene A., Laucys V., Janulaitis A.A.; RL Unpublished observations. RN [2] RA Janulaitis A.A., Marcinkeviciene L.Y., Petrusyte M.P.; RL Dokl. Akad. Nauk SSSR 262:241-244(1982). // More detailed explanations for each field can be found in the accompanying user manual file, 'bairoch.doc'. ****************************************************************************** #20. DNASIS GET FILE(S): dnasis.### DESCRIPTION: restriction enzyme data file formatted for use with DNASIS. This file contains EOLN (end of line) characters which get lost via email and while ftping in ascii transfer mode. So for best results, ftp it using binary mode. For versions of DNASIS that cannot handle enzyme entries of 25 characters or more, try dnasis5.### (In this file, the longer rows have been omitted.) EXAMPLE: # of enzymes to be listed restriction enzyme name recognition sequence, cut site marked with a "!" 333 AatI AGG!CCT AatII GACGT!C Acc65I G!GTACC AccI GT!MKAC AccII CG!CG AccIII T!CCGGA ****************************************************************************** #21. PUBLISHED REFERENCES GET FILE(S): pubrefs.### (new-this-month), pubrefsa.### (LARGE file! 7MB+-) DESCRIPTION: all the published references stored in REBASE complete with abstracts. A monthly update file of the additions and the modifications to this file is maintained. EXAMPLE: <1> <2> <3> <journal> or <book, publisher, editor, city> <4> <volume> <5> <pages> <6> <year> <7> <abstract> <> <1>Sanders, M.E., Klaenhammer, T.R. <2>Phage resistance in a phage-insensitive strain of Streptococcus lactis: temperature-dependent phage development and host-controlled phage replication <3>Appl. Environ. Microbiol. <4>47 <5>979-985 <6>1984 <7>Streptococcus lactis ME2 is a dairy starter strain that is insensitive to a variety of phage, including Phi18. The efficiency of plating of Phi18 on ME2 and N1 could be increased from <1 X 10-9 to 5.0 X 10-2 and from 7.6 X 10-7 to 2.1 X 10-2, respectively, when the host strains were subcultured at 40C before plating the phage and the phage assay plates were incubated at 40C. Host-dependent replication was demonstrated in N1 at 30C and in N1 and ME2 at 40C, suggesting the operation of a temperature-sensitive restriction and modification system in MER2 and N1. The increased sensitivity of ME2 and N1 to Phi18 at 40C was also demonstrated by lysis of broth cultures and increase in plaque size. ME2 grown at 40C showed an increased ability to adsorb Phi18 indicating a second target for temperature-dependent phage sensitivity in ME2. Challenge of N1 with a Phi18 preparation that had been previously modified for growth on N1 indicated that at 40C phage development was characterized by a shorter latent period and larger burst size than at 30C. The evidence presented suggests that the high degree of phage insensitivity expressed by ME2 consists of a variety of temperature-sensitive mechanisms, including (i) the prevention of phage adsorption, (ii) host-controlled restriction of phage, and (iii) suppression of phage development. At 30C these factors appear to act cooperatively to prevent the successful emergence of lytic phage active against S. lactis ME2. <> ****************************************************************************** #22. PROCITE REFERENCES GET FILE(S): procite.### (new-this-month), procitea.### (LARGE file! 7MB+-) DESCRIPTION: all the published references stored in REBASE complete with abstracts, formatted for use with Pro-Cite software. A monthly update of the additions and modifications to this file is maintained. Also, usable with EndNote. These files contain binary characters that do not survive email. Thus, for best results, retrieve it from our ftp site. EXAMPLE: For a journal article: @D<tab>Author1//Author2 <tab>Title<tab>Journal<tab>Year<tab>Volume<tab> <tab>Pages<tab><tab><tab>Abstract<tab><tab><return> For a book article: @A<tab>Author1//Author2 <tab><tab>Title<tab><tab><tab>Editor1//Editor2 <tab> <tab>Book<tab><tab><tab><tab>City<tab>Publisher<tab>Year<tab><tab>Volume <tab><tab>Pages<tab><tab><tab><tab><tab><tab><tab><tab><tab>Abstract<tab> <tab><return> @D\tHo, D.K.//Wu, J.C.//Santi, D.V.//Floss, H.G.\tStereochemical studies of the C-methylation of deoxycytidine catalyzed by Hhal methylase and the N-methylation of deoxyadenosine catalyzed by EcoRI methylase.\tArch. Biochem. Biophys.\t1991\t284\t264-269\t\t\tThe steric course of methyl group transfer catalyzed by two DNA methylases, HhaI methylase, a DNA (cytosine-5) methyltransferase, and EcoRI methylase, which methylates at N6 of adenosine, has been studied with (methyl-R)- and (methyl-S)-[methyl-2H1,3H] adenosylmethionine as the methyl donor, using as substrates poly-d(GC) (HhaI) and the dodecamer oligonucleotide duplex d(CGCGAATTCGCG) (EcoRI), respectively. The methylated nucleotides were degraded to convert the chiral methyl groups into acetic acid for configurational analysis. It was found that both enzymatic reactions proceed with inversion of configuration of the methyl group.\t\t ****************************************************************************** #23. GENEPRO FORMAT GET FILE(S): genepro.### DESCRIPTION: enzyme datafile designed for use with GENEPRO software. EXAMPLE: <enzyme name> $ tab # <recognition sequence with cut sites marked> * newline AaaI$ #4C^GGCCG* AacI$ #4GGATCC* AaeI$ #4GGATCC* AagI$ #4AT^CGAT* AatI$ #4AGG^CCT* AatII$ #4GACGT^C* AbrI$ #4C^TCGAG* AcaI$ #4TTCGAA* AcaII$ #4GGATCC* AcaIII$ #4TGCGCA* ****************************************************************************** #24. GENEPRO FORMAT (commercial) GET FILE(S): geneproc.### DESCRIPTION: enzyme datafile designed for use with GENEPRO software. Differs from the regular genepro format in that only commercially available enzymes are listed. EXAMPLE: <enzyme name> $ tab # <recognition sequence with cut sites marked> * newline AaaI$ #4C^GGCCG* AacI$ #4GGATCC* AaeI$ #4GGATCC* AagI$ #4AT^CGAT* AbrI$ #4C^TCGAG* AcaI$ #4TTCGAA* AcaII$ #4GGATCC* AcaIII$ #4TGCGCA* AcaIV$ #4GGCC* Acc38I$ #4CCWGG* ****************************************************************************** #25. REBASE NEWS GET FILE(S): NEWS.### DESCRIPTION: Our monthly newsletter. Reports any notable changes since the previous REBASE version, such as any enzyme name changes, announcements of new REBASE formats, new commercial suppliers, corrections, etc. Automatically sent to each subscriber of any of our formats. Serves as an email notification indicating that a new REBASE version is ready at our ftp and web sites. ****************************************************************************** #26. Prototypes and Their Neoschizomers GET FILE(S): neos.### DESCRIPTION: A list of Type I, II, and III prototypes together with an example of all neoschizomers known for each specificity. EXAMPLE: prototype recognition sequence with cleavage site neoschizomer recognition sequence with cleavage site ApaI GGGCC^C Bsp120I G^GGCCC ApaBI GCANNNNN^TGC ApaLI G^TGCAC ApoI R^AATTY AvaI C^YCGRG Nli387/7I CYCGR^G ****************************************************************************** #27. Reference Manager GET FILE(S): refmgr.### DESCRIPTION: REBASE references suitable for use with Reference Manager. EXAMPLE: TY - Type of reference AU - Authors, listed one per line TI - Title JO - Journal PY - Year SP - Starting page EP - Ending page VL - Volume number AB - Abstract ER - End of Record TY - JOUR AU - Bae M. AU - Suh W.-N. AU - Song E.-S. AU - Lee K.-J. TI - Numerical identification of a Streptomyces strain producing restriction endonuclease SdiI. JO - Korean J. Appl. Microbiol. Biotechnol. PY - 1994 SP - 126 EP - 133 VL - 22 AB - Numerical identification was applied for Streptomyces sp. 264, an isolate AB producing a new restriction endonuclease SdiI. The restriction enzyme AB - would appear to be an isoschizomer of XhoI. Fifty taxonomic unit AB - characters were tested and the data obtained were analyzed numerically AB - by using the TAXON program. The isolate was identified to be the major AB - cluster 19 of Streptomyces and best matched to S. diastatochromogenes. AB - It was, therefore, concluded that the isolate was identified to be a AB - member of Streptomyces diastatochromogenes. ER - ****************************************************************************** #28. SEQAIDII FORMAT GET FILE(S): seqaidii.### DESCRIPTION: Enzymes sorted according to the number of bases in the recognition site formatted for use with the SEQAIDII program. EXAMPLE: <# of bases>,<enzyme name>,<recognition sequence>,<offset> 10,BsaBI,GATNNNNATC,+4 10,MslI,CAYNNNNRTG,+4 10,PshAI,GACNNNNGTC,+4 10,XmnI,GAANNNNTTC,+4 11,AhdI,GACNNNNNGTC,+5 11,ApaBI,GCANNNNNTGC,+7 11,BglI,GCCNNNNNGGC,+6 11,BsiYI,CCNNNNNNNGG,+6 11,BslI,CCNNNNNNNGG,+6 11,CjeI,CCANNNNNNGT,+19,ACNNNNNNTGG,-16 11,Eam1105I,GACNNNNNGTC,+5 11,EcoNI,CCTNNNNNAGG,+4 11,MwoI,GCNNNNNNNGC,+6 11,PflMI,CCANNNNNTGG,+6 12,BcgI,GCANNNNNNTCG,+23,CGANNNNNNTGC,-11 12,Bsp24I,GACNNNNNNTGG,+23,CCANNNNNNGTC,-8 12,BstXI,CCANNNNNNTGG,+7 12,CjePI,CCANNNNNNNTC,+19,GANNNNNNNTGG,-15 12,DrdI,GACNNNNNNGTC,+6 ****************************************************************************** #29. GENETYX FORMAT GET FILE(S): genetyx.### DESCRIPTION: REBASE enzyme data file for use with GENETYX. EXAMPLE: <enzyme>,<recognition sequence with cleavage site> "+" indicates a non palindromic entry AatII,GACGT|C Acc65I,G|GTACC AccI,GT|MKAC +AceIII,CAGCTC(7/11) +AciI,CCGC(-3/-1) AclI,AA|CGTT AcyI,GR|CGYC AflII,C|TTAAG AflIII,A|CRYGT AgeI,A|CCGGT AhaIII,TTT|AAA AhdI,GACNNN|NNGTC AluI,AG|CT +AlwI,GGATC(4/5) AlwNI,CAGNNN|CTG ApaBI,GCANNNNN|TGC ****************************************************************************** #30. IG Suite format (commercial) GET FILE(S): bionetc.### DESCRIPTION: enzyme file like format #13 but with commercial enzymes only. ****************************************************************************** #31. ALL ENZYMES (INDIVIDUALLY REFERENCED) WITH ISOSCHIZOMERS GET FILE(S): withrefm.### (LARGE file. 2MB+) DESCRIPTION: Similar to format #10, except that instead of just the prototype, all isoschizomers are given. ****************************************************************************** #32. Type II with Isoschizomers (commercial) GET FILE(S): gtype2c.###, type2ref.### DESCRIPTION: Like format #7, but with only one of each commercially available specificity. ****************************************************************************** #33. CAD Gene FORMAT GET FILE(S): cadgene.### DESCRIPTION: REBASE enzyme data file for use with CAD Gene software. EXAMPLE: Field 1 Enzyme Field 2 Recognition sequence Field 3 Cut site (for non-palindromes, a 2nd cut site appears here) Field 4 & 5 True if commercially available, otherwise false (T/F) Field 6 Commercial sources AceI, GCWGC, 1, F, F, AceII, GCTAGC, 5, F, F, AceIII, CAGCTC, 13, 17, F, F, AciI, CCGC, 1, 3, T, T, N AclI, AACGTT, 2, T, T, I AclNI, ACTAGT, 1, T, T, I AclWI, GGATC, 9, 10, T, T, I ****************************************************************************** #34. HOMING ENDONUCLEASES GET FILE(S): homing.### DESCRIPTION: a list of intron-encoded endonucleases, their recognition sequences (cut sites shown), and their commercial sources. EXAMPLE: ^ indicates cleavage position on the strand shown _ indicates cleavage position on the complementary strand Enzyme 5' Recognition Sequence Commercial Sources HO-endo 5' CTTTCCGC_AACA^GTATAATT I-CeuI 5' TCTAACTATAACGGTC_CTAA^GGTAGCGAG N I-PpoI 5' TAACTATGACTCTC_TTAA^GGTAGCCAAAAG NR ****************************************************************************** #35. Clone Manager GET FILE(S): clonemgr.### DESCRIPTION: datafile for Scientific & Educational Software's Clone Manager Clone 5 can import this file directly. To update older versions of Clone Manager, visit the Sci-Ed web site (www.scied.com) ****************************************************************************** #36. Gene Runner GET FILE(S): generunr.### DESCRIPTION: use this file to update your Gene Runner enzyme list EXAMPLE: enzyme recognition sequence comments (supplier list) "AaaI" "C/GGCCG" O "" "" "AagI" "AT/CGAT" O "" "" "AatI" "AGG/CCT" O "" "O" "AatII" "GACGT/C" O "" "A,D,E,F,K,L,M,N,O,R" "AccII" "CG/CG" O "" "A,J,K,Q" NOTE: In order to use Gene Runner's search-by-supplier feature, you will also need to download these files: A.rst - Amersham Pharmacia Biotech B.rst - Life Technologies Inc. C.rst - Minotech, Molecular Biology Products D.rst - Angewandte Gentechnologie Systeme E.rst - Stratagene F.rst - Fermentas AB G.rst - Appligene Oncor H.rst - American Allied Biochemical, Inc. I.rst - SibEnzyme Ltd. J.rst - Nippon Gene Co., Ltd. K.rst - Takara Shuzo Co. Ltd. L.rst - Kramel Biotech M.rst - Roche Molecular Biochemicals N.rst - New England BioLabs O.rst - Toyobo Biochemicals P.rst - Megabase Research Products Q.rst - CHIMERx R.rst - Promega Corporation S.rst - Sigma Chemical Corporation T.rst - Advanced Biotechnologies Ltd. ****************************************************************************** #37. EMBOSS GET FILE(S): emboss_e.###, emboss_s.###, emboss_r.### DESCRIPTION: Use these files with the open source package called EMBOSS (the European Molecular Biology Open Software Suite) For more information visit: http://www.sanger.ac.uk/Software/EMBOSS ****************************************************************************** #38. Bairoch-Mini (MacVector, Vector NTI, PC/Gene) GET FILE(S): bairoch.doc, bairochc.### DESCRIPTION: a subset of the regular bairoch file (format #19) - an alphabetical listing of commercially available type II restriction enzymes, in a format that is compatible with PROSITE, SWISS-PROT, EMBL, ENZYME, ECD, EPD, HAEMB data banks. To import this file into MacVector, download Oxford Molecular's Group's free REBASE->MacVector utility: http://www.accelrys.com/products/macvector/rebase_converter.html ****************************************************************************** OTHER DATA FORMATS: Gene Construction Kit and Gene Inspector: Updated enzyme files can be obtained from their web site, www.textco.com (or by sending email to info@textco.com). DNAStar: Data files can be obtained via email (support@dnastar.com) or by calling (608)258-7420 (ask for tech support). Sequencher: Contact Gene Codes at www.genecodes.com for information relating to Sequencher data files. ------------------------------------------------------------------------------ <end of REBASE.DOC>