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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.
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.
% 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
Standard (Mandatory) qualifiers:
[-infile] infile Full pathname of WITHREFM file
[-protofile] infile Full pathname of PROTO file
Additional (Optional) qualifiers:
-[no]equivalences boolean This option calculates an embossre.equ file
using restriction enzyme prototypes in the
withrefm file.
Advanced (Unprompted) 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 standard and additional values
-debug boolean Write debug output to program.dbg
-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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-infile] (Parameter 1) |
Full pathname of WITHREFM file | Input file | Required |
| [-protofile] (Parameter 2) |
Full pathname of PROTO file | Input file | Required |
| Additional (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 (Unprompted) 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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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
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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:
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.
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 |