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rebaseextract |
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.
% 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
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) |
For example, the withrefm file for REBASE version 005 is at: ftp://ftp.neb.com/pub/rebase/withrefm.005
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. |
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The output files are held in the REBASE subdirectory of the EMBOSS data directory. There are three:
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
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 |