EMBOSS: rebaseextract


Program rebaseextract

Function

Extract data from REBASE

Description

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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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. Most 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/

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.

Usage

Here is a sample session with rebaseextract.

% rebaseextract
Full pathname of WITHREFM: /data/rebase/withrefm.904


Command line arguments

   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)

Input file format

The input file must be the "withrefm" file of a REBASE distribution.

For example, the withrefm file for REBASE version 005 is at: ftp://ftp.neb.com/pub/rebase/withrefm.005

Output file format

The output files are held in the REBASE subdirectory of the EMBOSS data directory. There are three: Here are examples of the three formats:

Data files

The "withrefm" file of an REBASE distribution is the input file for this program.

Notes

The home page of REBASE is: http://rebase.neb.com/

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

References

  1. Nucleic Acids Research 27: 312-313 (1999).

Warnings

The program will warn you if the input file is incorrectly formatted.

Diagnostic Error Messages

Exit status

It exits with status 0 unless an error is reported.

Known bugs

See also

Program nameDescription
cutgextractExtract data from CUTG
domainerBuild domain coordinate files
nrscopeConverts redundant EMBL-format SCOP file to non-redundant one
pdbtospConvert raw swissprot:pdb equivalence file to embl-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
scopeConvert raw scop classification file to embl-like format
scopparseReads raw-, and writes EMBL-like, scop classification files
seqnrConverts redundant database results to a non-redundant set of hits
tfextractExtract data from TRANSFAC

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Completed 12th April 1999

Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

Comments