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redata |
The home page of REBASE is: http://rebase.neb.com/
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]: BamHI Output file [outfile.redata]: |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-enzyme] string [BamHI] Enter the name of the restriction
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-independent ('AaeI' is the same as
'aaei') (Any string is accepted)
[-outfile] outfile [*.redata] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-[no]isoschizomers boolean [Y] Show other enzymes with this
specificity. (Isoschizomers)
-[no]references boolean [Y] Show references
-[no]suppliers boolean [Y] Show suppliers
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 string Output directory
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 dying program messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-enzyme] (Parameter 1) |
Enter the name of the restriction 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-independent ('AaeI' is the same as 'aaei') | Any string is accepted | BamHI |
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.redata |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]isoschizomers | Show other enzymes with this specificity. (Isoschizomers) | Boolean value Yes/No | Yes |
| -[no]references | Show references | Boolean value Yes/No | Yes |
| -[no]suppliers | Show suppliers | Boolean value 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 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 Suppliers: Amersham Pharmacia Biotech (1/01) Life Technologies Inc. (1/98) Minotech, Molecular Biology Products (12/00) HYBAID GmbH (12/00) Stratagene (11/00) Fermentas AB (5/01) Q-BIOgene (1/01) American Allied Biochemical, Inc. (10/98) SibEnzyme Ltd. (1/01) Nippon Gene Co., Ltd. (6/00) Takara Shuzo Co. Ltd. (2/01) Transgenomic Ltd. (1/01) Roche Molecular Biochemicals (1/01) New England BioLabs (12/00) Toyobo Biochemicals (11/98) CHIMERx (10/97) Promega Corporation (6/99) Sigma Chemical Corporation (11/98) Advanced Biotechnologies Ltd. (3/98) Bangalore Genei (2/01) MRC-Holland (3/01) 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. |
This includes the full list of isoschizomers (enzymes with the same target sequence), suppliers and references from the REBASE database.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
The EMBOSS REBASE restriction enzyme data files are stored iin directory 'data/REBASE/*' under the EMBOSS installation directory.
These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager.
The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are:
The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish.
The format of the file "embossre.equ" is
Enzyme-name Prototype-name
i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name.
| Program name | Description |
|---|---|
| recoder | Remove restriction sites but maintain same translation |
| remap | Display sequence with restriction sites, translation etc |
| restover | Find restriction enzymes producing specific overhang |
| restrict | Finds restriction enzyme cleavage sites |
| showseq | Display a sequence with features, translation etc |
| silent | Silent mutation restriction enzyme scan |