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EMBOSS: rebaseextract |
The home page of REBASE is: http://rebase.neb.com/
This program derives recognition site and cleavage information from the "withrefm" file of an REBASE distribution. It creates three files in the EMBOSS data subdirectory REBASE. A pattern file, a reference file and a supplier file.
The EMBOSS programs that find restriction cutting sites use the data files produced by this program and will not work without them.
Running this program may be the job of your system manager.
% rebaseextract Full pathname of WITHREFM: /data/rebase/withrefm.904
Mandatory qualifiers: [-inf] infile Full pathname of WITHREFM Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-inf] (Parameter 1) |
Full pathname of WITHREFM | Input file | Required |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
For example, the withrefm file for REBASE version 005 is at: ftp://ftp.neb.com/pub/rebase/withrefm.005
# length cuts blunt 3' 5' [3'] [5'] AlwI GGATC 5 2 0 9 10 0 0 Alw21I GWGCWC 6 2 0 5 1 0 0 Alw26I GTCTC 5 2 0 6 10 0 0 Alw44I GTGCAC 6 2 0 1 5 0 0
# 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) # AclI Acinetobacter calcoaceticus M4 Psp1406I ?(5) S.K. Degtyarev IN 1 Nucleic Acids Res. vol. 20 pp. 3787. //
# REBASE Supplier information for EMBOSS # # Format: # Code of Supplier<ws>Supplier name # A Amersham Pharmacia Biotech (11/98) B Life Technologies Inc. (1/98) C Minotech, Molecular Biology Products (3/99) D Angewandte Gentechnologie Systeme (10/97) E Stratagene (1/98) F Fermentas AB (1/99) G Appligene Oncor (10/97) H American Allied Biochemical, Inc. (10/98) I SibEnzyme Ltd. (3/99) J Nippon Gene Co., Ltd. (10/97) K Takara Shuzo Co. Ltd. (11/98) L Kramel Biotech (7/98) M Roche Molecular Biochemicals (3/99) N New England BioLabs (3/99) O Toyobo Biochemicals (11/98) P Megabase Research Products (3/99) Q CHIMERx (10/97) R Promega Corporation (10/98) S Sigma Chemical Corporation (11/98) T Advanced Biotechnologies Ltd. (3/98)
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
Program name | Description |
---|---|
cutgextract | Extract data from CUTG |
domainer | Build domain coordinate files |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
scope | Convert raw scop classification file to embl-like format |
scopparse | Reads raw-, and writes EMBL-like, scop classification files |
seqnr | Converts redundant database results to a non-redundant set of hits |
tfextract | Extract data from TRANSFAC |