rebaseextract.output

emboss的linux版本的源代码

<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: REBASE</h3>
<p>This directory contains output files, for example embossre.enz embossre.equ embossre.ref and embossre.sup.
<p><h3>File: REBASE/embossre.enz</h3>
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<pre>
# REBASE enzyme patterns for EMBOSS
#
# Format:
# name&lt;ws&gt;pattern&lt;ws&gt;len&lt;ws&gt;ncuts&lt;ws&gt;blunt&lt;ws&gt;c1&lt;ws&gt;c2&lt;ws&gt;c3&lt;ws&gt;c4
#
# Where:
# name = name of enzyme
# pattern = recognition site
# len = length of pattern
# ncuts = number of cuts made by enzyme
#         Zero represents unknown
# blunt = true if blunt end cut, false if sticky
# c1 = First 5' cut
# c2 = First 3' cut
# c3 = Second 5' cut
# c4 = Second 3' cut
#
# Examples:
# AAC^TGG -&gt; 6 2 1 3 3 0 0
# A^ACTGG -&gt; 6 2 0 1 5 0 0
# AACTGG  -&gt; 6 0 0 0 0 0 0
# AACTGG(-5/-1) -&gt; 6 2 0 1 5 0 0
# (8/13)GACNNNNNNTCA(12/7) -&gt; 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
</pre>
</td></tr></table><p>
<p><h3>File: REBASE/embossre.equ</h3>
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<pre>
Bsc4I BsiYI
Bse1I BsrI
BshI HaeIII
BsiSI HpaII
Bsu6I Ksp632I
HpyCH4IV MaeII
</pre>
</td></tr></table><p>
<p><h3>File: REBASE/embossre.ref</h3>
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<pre>
# 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,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,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,Bsp98I,Bsp130I,Bsp131I,Bsp144I,Bsp4009I,BspAAIII,BstI,Bst1126I,Bst2464I,Bst2902I,BstQI,Bsu90I,Bsu8565I,Bsu8646I,BsuB519I,BsuB763I,CelI,DdsI,GdoI,GinI,GoxI,GseIII,MleI,Mlu23I,NasBI,Nsp29132II,NspSAIV,OkrAI,Pac1110I,Pae177I,Pfl8I,Psp56I,RhsI,Rlu4I,RspLKII,SolI,SpvI,SurI,Uba19I,Uba31I,Uba38I,Uba51I,Uba88I,Uba1098I,Uba1163I,Uba1167I,Uba1172I,Uba1173I,Uba1205I,Uba1224I,Uba1242I,Uba1250I,Uba1258I,Uba1297I,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.


<font color=red>  [Part of this file has been deleted for brevity]</font>

ATCC 49790
ABCDEFGHIJKLMNOQRSTU
3
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.
//
Ksp632I
Kluyvera species 632
Bco5I,Bco116I,BcoKI,BcoSI,BcrAI,BseZI,BsrEI,Bst6I,Bst158I,Bsu6I,Eam1104I,EarI,TdeII,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 &amp; Nucleotides, 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., Schmitt, 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,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
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 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.
//
</pre>
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<p><h3>File: REBASE/embossre.sup</h3>
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<pre>
# REBASE Supplier information for EMBOSS
#
# Format:
# Code of Supplier&lt;ws&gt;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)
</pre>
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