rebaseextract.txt

emboss的linux版本的源代码

# c3 = Second 5' cut
# c4 = Second 3' cut
#
# Examples:
# AAC^TGG -> 6 2 1 3 3 0 0
# A^ACTGG -> 6 2 0 1 5 0 0
# AACTGG  -> 6 0 0 0 0 0 0
# AACTGG(-5/-1) -> 6 2 0 1 5 0 0
# (8/13)GACNNNNNNTCA(12/7) -> 12 4 0 -9 -14 24 19
#
# i.e. cuts are always to the right of the given
# residue and sequences are always with reference to
# the 5' strand.
# Sequences are numbered ... -3 -2 -1 1 2 3 ... with
# the first residue of the pattern at base number 1.
#
AaeI    ggatcc  6       0       0       0       0       0       0
AciI    CCGC    4       2       0       1       3       0       0
AclI    AACGTT  6       2       0       2       4       0       0
BamHI   GGATCC  6       2       0       1       5       0       0
BceAI   ACGGC   5       2       0       17      19      0       0
Bsc4I   CCNNNNNNNGG     11      2       0       7       4       0       0
Bse1I   ACTGG   5       2       0       6       4       0       0
BseYI   CCCAGC  6       2       0       1       5       0       0
BshI    GGCC    4       2       1       2       2       0       0
BsiSI   CCGG    4       2       0       1       3       0       0
BsiYI   CCNNNNNNNGG     11      2       0       7       4       0       0
BssKI   CCNGG   5       2       0       -1      5       0       0
BsrI    ACTGG   5       2       0       6       4       0       0
Bsu6I   CTCTTC  6       2       0       7       10      0       0
ClaI    ATCGAT  6       2       0       2       4       0       0
EcoRI   GAATTC  6       2       0       1       5       0       0
EcoRII  CCWGG   5       2       0       -1      5       0       0
HaeIII  GGCC    4       2       1       2       2       0       0
HhaI    GCGC    4       2       0       3       1       0       0
Hin4I   GAYNNNNNVTC     11      4       0       -9      -14     24      19
Hin6I   GCGC    4       2       0       1       3       0       0
HinP1I  GCGC    4       2       0       1       3       0       0
HindI   cac     3       0       0       0       0       0       0
HindII  GTYRAC  6       2       1       3       3       0       0
HindIII AAGCTT  6       2       0       1       5       0       0
HpaII   CCGG    4       2       0       1       3       0       0
HpyCH4IV        ACGT    4       2       0       1       3       0       0
HspAI   GCGC    4       2       0       1       3       0       0
KpnI    GGTACC  6       2       0       5       1       0       0
Ksp632I CTCTTC  6       2       0       7       10      0       0
MaeII   ACGT    4       2       0       1       3       0       0
NotI    GCGGCCGC        8       2       0       2       6       0       0
TaqI    TCGA    4       2       0       1       3       0       0

  File: REBASE/embossre.equ

Bsc4I BsiYI
Bse1I BsrI
BshI HaeIII
BsiSI HpaII
Bsu6I Ksp632I
HpyCH4IV MaeII

  File: REBASE/embossre.ref

# REBASE enzyme information for EMBOSS
#
# Format:
# Line 1: Name of Enzyme
# Line 2: Organism
# Line 3: Isoschizomers
# Line 4: Methylation
# Line 5: Source
# Line 6: Suppliers
# Line 7: Number of following references
# Lines 8..n: References
# // (end of entry marker)
#
AaeI
Acetobacter aceti sub. liquefaciens
BamHI,AacI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II
,BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,
Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902
I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,Gse
III,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,Rh
sI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba
1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,U
ba1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I
,Uba1402I,Uba1414I

M. Van Montagu

1
Seurinck, J., van Montagu, M., Unpublished observations.
//
AciI
Arthrobacter citreus

?(5),-2(5)
NEB 577
N
2
Lunnen, K.D., Heiter, D., Wilson, G.G., Unpublished observations.
Polisson, C., Morgan, R.D., (1990) Nucleic Acids Res., vol. 18, pp. 5911.
//
AclI
Acinetobacter calcoaceticus M4
Psp1406I
3(5)
S.K. Degtyarev
IN
2
Degtyarev, S.K., Abdurashitov, M.A., Kolyhalov, A.A., Rechkunova, N.I., (1992)
Nucleic Acids Res., vol. 20, pp. 3787.
Lunnen, K.D., Wilson, G.G., Unpublished observations.
//
BamHI
Bacillus amyloliquefaciens H
AacI,AaeI,AcaII,AccEBI,AinII,AliI,Ali12257I,Ali12258I,ApaCI,AsiI,AspTII,Atu1II,
BamFI,BamKI,BamNI,Bca1259I,Bce751I,Bco10278I,BnaI,BsaDI,Bsp30I,Bsp46I,Bsp90II,B
sp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I
,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseI
II,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,Rhs
I,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1
163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Ub
a1297I,Uba1302I,Uba1324I,Uba1325I,Uba1334I,Uba1339I,Uba1346I,Uba1383I,Uba1398I,
Uba1402I,Uba1414I
5(4)
ATCC 49763
ABCDEFGHIJKLMNOQRSTUV
10
Brooks, J.E., Howard, K.A., US Patent Office, 1994.


  [Part of this file has been deleted for brevity]

ATCC 49790
ABCDEFGHIJKLMNOQRSTU
3
Kiss, A., Finta, C., Venetianer, P., (1991) Nucleic Acids Res., vol. 19, pp. 34
60.
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.
//
Ksp632I
Kluyvera species 632
Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,T
deII,Uba1192I,Uba1276I,VpaKutEI,VpaKutFI,VpaO5I

DSM 4196
M
2
Bolton, B.J., Schmitz, G.G., Jarsch, M., Comer, M.J., Kessler, C., (1988) Gene,
 vol. 66, pp. 31-43.
Tsukahara, S., Yamakawa, H., Takai, K., Takaku, H., (1994) Nucleosides & Nucleo
tides, vol. 13, pp. 1617-1626.
//
MaeII
Methanococcus aeolicus PL-15/H
HpyCH4IV,HpyF13III,HpyF35II,HpyF74II,TaiI,TscI,Tsp49I,TspIDSI,TspWAM8AI,TtmI

K.O. Stetter
M
1
Schmid, K., Thomm, M., Laminet, A., Laue, F.G., Kessler, C., Stetter, K.O., Sch
mitt, R., (1984) Nucleic Acids Res., vol. 12, pp. 2619-2628.
//
NotI
Nocardia otitidis-caviarum
CciNI,CspBI,MchAI
?(4)
ATCC 14630
ABCDEFGHJKLMNOQRSTU
4
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.
//
TaqI
Thermus aquaticus YTI
CviSIII,EsaBC3I,HpyV,Hpy26II,HpyF14III,HpyF16I,HpyF23I,HpyF24I,HpyF26III,HpyF30
I,HpyF35I,HpyF40II,HpyF42IV,HpyF45I,HpyF49I,HpyF52I,HpyF59III,HpyF62II,HpyF64I,
HpyF65II,HpyF66IV,HpyF71I,HpyF73II,HpyJP26II,PpaAII,Taq20I,Tbr51I,TfiA3I,TfiTok
4A2I,TfiTok6A1I,TflI,Tsc4aI,Tsp32I,Tsp32II,Tsp358I,Tsp505I,Tsp510I,TspAK13D21I,
TspAK16D24I,TspNI,TspVi4AI,TspVil3I,Tth24I,TthHB8I,TthRQI
4(6)
J.I. Harris
ABCDEFGIJLMNOQRSTU
5
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.
//

  File: REBASE/embossre.sup

# REBASE Supplier information for EMBOSS
#
# Format:
# Code of Supplier<ws>Supplier name
#
A Amersham Pharmacia Biotech (1/01)
B Life Technologies Inc. (1/98)
C Minotech, Molecular Biology Products (12/00)
D HYBAID GmbH (12/00)
E Stratagene (11/00)
F Fermentas AB (5/01)
G Q-BIOgene (1/01)
H American Allied Biochemical, Inc. (10/98)
I SibEnzyme Ltd. (1/01)
J Nippon Gene Co., Ltd. (6/00)
K Takara Shuzo Co. Ltd. (2/01)
L Transgenomic Ltd. (1/01)
M Roche Molecular Biochemicals (1/01)
N New England BioLabs (12/00)
O Toyobo Biochemicals (11/98)
P Megabase Research Products (5/99)
Q CHIMERx (10/97)
R Promega Corporation (6/99)
S Sigma Chemical Corporation (11/98)
T Advanced Biotechnologies Ltd. (3/98)
U Bangalore Genei (2/01)
V MRC-Holland (3/01)

   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

   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.

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    Build the PROSITE motif database for use by patmatmotifs
   tfextract      Extract data from TRANSFAC

Author(s)

   Alan Bleasby (ajb