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EMBOSS: redata |
The home page of REBASE is: http://rebase.neb.com/rebase/rebase.html
This program searches the REBASE database for information on a specified restriction enzyme.
It outputs a report including the cut site, isoschizomers, references and commercial suppliers of the enzyme.
% redata Search REBASE for enzyme name, references, suppliers etc. Restriction enzyme name [BamHI]: Output file [outfile.redata]:
Mandatory qualifiers: [-enzyme] string Enter the name of the restrcition enzyme that you wish to get details of. The names often have a 'I' in them - this is a capital 'i', not a '1' or an 'l'. The names are case-indeppendent ('AaeI' is the same as 'aaei') [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -[no]isoschizomers bool Show other enzymes with this specificity. (Isoschizomers) -[no]references bool Show references -[no]suppliers bool Show suppliers |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-enzyme] (Parameter 1) |
Enter the name of the restrcition enzyme that you wish to get details of. The names often have a 'I' in them - this is a capital 'i', not a '1' or an 'l'. The names are case-indeppendent ('AaeI' is the same as 'aaei') | Any string is accepted | BamHI |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.redata |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-[no]isoschizomers | Show other enzymes with this specificity. (Isoschizomers) | Yes/No | Yes |
-[no]references | Show references | Yes/No | Yes |
-[no]suppliers | Show suppliers | Yes/No | Yes |
BamHI Recognition site is GGATCC leaving sticky ends Cut positions 5':1 3':5 Organism: Bacillus amyloliquefaciens H Methylated: 5(4) Source: ATCC 49763 Isoschizomers: 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 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 Suppliers: Amersham Pharmacia Biotech (11/98) Life Technologies Inc. (1/98) Minotech, Molecular Biology Products (3/99) Angewandte Gentechnologie Systeme (10/97) Stratagene (1/98) Fermentas AB (8/99) Appligene Oncor (10/97) American Allied Biochemical, Inc. (10/98) SibEnzyme Ltd. (9/99) Nippon Gene Co., Ltd. (10/97) Takara Shuzo Co. Ltd. (11/98) Kramel Biotech (7/98) Roche Molecular Biochemicals (3/99) New England BioLabs (2/00) Toyobo Biochemicals (11/98) CHIMERx (10/97) Promega Corporation (6/99) Sigma Chemical Corporation (11/98) Advanced Biotechnologies Ltd. (3/98) References: Brooks, J.E., Howard, K.A., US Patent Office, 1994. Brooks, J.E., Nathan, P.D., Landry, D., Sznyter, L.A., Waite-Rees, P., Ives, C.L., Moran, L.S., Slatko, B.E., Benner, J.S., (1991) Nucleic Acids Res., vol. 19, pp. 841-850. Hattman, S., Keister, T., Gottehrer, A., (1978) J. Mol. Biol., vol. 124, pp. 701-711. Lee, S.P., Porter, D., Chirikjian, J.G., Knutson, J.R., Han, M.K., (1994) Anal. Biochem., vol. 220, pp. 377-383. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I., Aggarwal, A.K., (1994) Structure, vol. 2, pp. 439-452. Roberts, R.J., Wilson, G.A., Young, F.E., (1977) Nature, vol. 265, pp. 82-84. Roy, K.B., Vrushank, D., Jayaram, B., (1994) Anal. Biochem., vol. 220, pp. 160-164. Strzelecka, T., Newman, M., Dorner, L.F., Knott, R., Schildkraut, I., Aggarwal, A.K., (1994) J. Mol. Biol., vol. 239, pp. 430-432. Wilson, G.A., Young, F.E., (1975) J. Mol. Biol., vol. 97, pp. 123-125. Xu, S.-Y., Fomenkov, A., (1994) Biotechniques, vol. 17, pp. 57.
These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager.
Program name | Description |
---|---|
chaos | Create a chaos game representation plot for a sequence |
cpgplot | Plot CpG rich areas |
cpgreport | Reports all CpG rich regions |
diffseq | Find differences (SNPs) between nearly identical sequences |
dotmatcher | Displays a thresholded dotplot of two sequences |
dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
einverted | Finds DNA inverted repeats |
equicktandem | Finds tandem repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
isochore | Plots isochores in large DNA sequences |
newcpgreport | Report CpG rich areas |
newcpgseek | Reports CpG rich regions |
palindrome | Looks for inverted repeats in a nucleotide sequence |
polydot | Displays all-against-all dotplots of a set of sequences |
rebaseextract | Extract data from REBASE |
remap | Display a sequence with restriction cut sites, translation etc |
restrict | Finds restriction enzyme cleavage sites |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |
tfscan | Scans DNA sequences for transcription factors |