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redata searches the REBASE database for information on a specified restriction enzyme. It writes an output file with information on the cut site and (optionally) the full list of isoschizomers (enzymes with the same target sequence), commercial suppliers of the enzyme and literature references.
% redata Retrieve information from REBASE restriction enzyme database Restriction enzyme name [BamHI]: BamHI Output file [outfile.redata]:
Go to the output files for this example
Retrieve information from REBASE restriction enzyme database Version: EMBOSS:220.127.116.11 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) [-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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 -version boolean Report version number and exit
|Standard (Mandatory) qualifiers|
|string||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||BamHI|
|outfile||Output file name||Output file||<*>.redata|
|Additional (Optional) qualifiers|
|Advanced (Unprompted) qualifiers|
|-[no]isoschizomers||boolean||Show other enzymes with this specificity. (Isoschizomers)||Boolean value Yes/No||Yes|
|-[no]references||boolean||Show references||Boolean value Yes/No||Yes|
|-[no]suppliers||boolean||Show suppliers||Boolean value Yes/No||Yes|
|"-outfile" associated outfile qualifiers|
|string||Output directory||Any string|
|-auto||boolean||Turn off prompts||Boolean value Yes/No||N|
|-stdout||boolean||Write first file to standard output||Boolean value Yes/No||N|
|-filter||boolean||Read first file from standard input, write first file to standard output||Boolean value Yes/No||N|
|-options||boolean||Prompt for standard and additional values||Boolean value Yes/No||N|
|-debug||boolean||Write debug output to program.dbg||Boolean value Yes/No||N|
|-verbose||boolean||Report some/full command line options||Boolean value Yes/No||Y|
|-help||boolean||Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose||Boolean value Yes/No||N|
|-warning||boolean||Report warnings||Boolean value Yes/No||Y|
|-error||boolean||Report errors||Boolean value Yes/No||Y|
|-fatal||boolean||Report fatal errors||Boolean value Yes/No||Y|
|-die||boolean||Report dying program messages||Boolean value Yes/No||Y|
|-version||boolean||Report version number and exit||Boolean value Yes/No||N|
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 in 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
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.
The Restriction Enzyme database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. More recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed.
The home page of REBASE is: http://rebase.neb.com/
redata uses the EMBOSS REBASE restriction enzyme data files stored in 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.
|recoder||Find restriction sites to remove (mutate) with no translation change|
|remap||Display restriction enzyme binding sites in a nucleotide sequence|
|restover||Find restriction enzymes producing a specific overhang|
|restrict||Report restriction enzyme cleavage sites in a nucleotide sequence|
|showseq||Display sequences with features in pretty format|
|silent||Find restriction sites to insert (mutate) with no translation change|
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.