
                              EMBOSS: restover
     _________________________________________________________________
   
                               Program restover
                                       
Function

   Finds restriction enzymes that produce a specific overhang
   
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   contains published and unpublished references, recognition and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/
   
   restover takes a specified sequence and a short sequence of a cut-site
   overhang and searches the REBASE database for matching enzymes that
   create the desired overhang sequence when they cut the input sequence.
   
Usage

   Here is a sample session with restover:

% restover
Finds restriction enzymes that produce a specific overhang
Input sequence(s): em:hsfau
Overlap sequence: cg
Output file [hsfau.restover]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-seqcomp]           string     Overlap sequence
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -min                integer    Minimum cuts per RE
   -max                integer    Maximum cuts per RE
   -single             bool       Force single site only cuts
   -threeprime         bool       3' overhang? (else 5') e.g. BamHI has CTAG
                                  as a 5' overhang, and ApaI has CCGG as 3'
                                  overhang.
   -[no]blunt          bool       Allow blunt end cutters
   -[no]sticky         bool       Allow sticky end cutters
   -[no]ambiguity      bool       Allow ambiguous matches
   -plasmid            bool       Allow circular DNA
   -[no]commercial     bool       Only enzymes with suppliers
   -datafile           string     Alternative RE data file
   -html               bool       Create HTML output
   -[no]limit          bool       Limits reports to one isoschizomer
   -preferred          bool       Report preferred isoschizomers
   -alphabetic         bool       Sort output alphabetically
   -fragments          bool       Show fragment lengths
   -name               bool       Show sequence name

   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
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-seqcomp]
   (Parameter 2) Overlap sequence Any string is accepted An empty string
   is accepted
   [-outfile]
   (Parameter 3) Output file name Output file <sequence>.restover
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -min Minimum cuts per RE Integer from 1 to 1000 1
   -max Maximum cuts per RE Integer up to 2000000000 2000000000
   -single Force single site only cuts Yes/No No
   -threeprime 3' overhang? (else 5') e.g. BamHI has CTAG as a 5'
   overhang, and ApaI has CCGG as 3' overhang. Yes/No No
   -[no]blunt Allow blunt end cutters Yes/No Yes
   -[no]sticky Allow sticky end cutters Yes/No Yes
   -[no]ambiguity Allow ambiguous matches Yes/No Yes
   -plasmid Allow circular DNA Yes/No No
   -[no]commercial Only enzymes with suppliers Yes/No Yes
   -datafile Alternative RE data file Any string is accepted An empty
   string is accepted
   -html Create HTML output Yes/No No
   -[no]limit Limits reports to one isoschizomer Yes/No Yes
   -preferred Report preferred isoschizomers Yes/No No
   -alphabetic Sort output alphabetically Yes/No No
   -fragments Show fragment lengths Yes/No No
   -name Show sequence name Yes/No No
   
Input file format

   It reads in a normal DNA sequence USA.
   
Output file format

   The output file from the above example is:
     _________________________________________________________________
   
# Restrict of HSFAU from 1 to 518
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2000000000
# Minimum length of recognition site: 2
# Number of hits with any overlap: 208
# Base Number   Enzyme          Site            5'      3'      [5'     3']
        11      TaqI            TCGA            11      13
        28      AciI            CCGC            25      27
        38      AciI            CCGC            38      40
        71      AciI            CCGC            71      73
        73      Hin6I           GCGC            73      75
        94      TaqI            TCGA            94      96
        103     BsiSI           CCGG            103     105
        162     BsiSI           CCGG            162     164
        190     Hin6I           GCGC            190     192
        192     Hin6I           GCGC            192     194
        225     Bse1I           ACTGG           221     219
        229     AciI            CCGC            226     228
        263     AciI            CCGC            263     265
        380     AciI            CCGC            377     379
        383     AciI            CCGC            380     382
        395     BsiSI           CCGG            395     397
        398     Hin6I           GCGC            398     400
        408     AclI            AACGTT          409     411
        409     HpyCH4IV        ACGT            409     411
     _________________________________________________________________
   
   The output from restover is a simple text one. The base number,
   restriction enzyme name, recognition site and cut positions are shown.
   Note that cuts are always to the right of the residue shown and that
   5' cuts are referred to by their associated 3' number sequence. The
   program reports enzymes that cut at two or four sites.
   
Data files

   The data files are stored in the REBASE directory of the standard
   EMBOSS data directory. The names are:
   
     * embossre.enz Cleavage information
     * embossre.ref Reference/methylation information
     * embossre.sup Supplier information
       
   The column information is described at the top of the data files
   
Notes

   The data files must have been created before running this program.
   This is done by running the rebaseextract program with the "withrefm"
   file from an REBASE release. You may have to ask your system manager
   to do this.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   recoder      Remove restriction sites but maintain the same translation
   redata       Search REBASE for enzyme name, references, suppliers etc
   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
   
Author(s)

   This application was written by Bernd Jagla bernd@golgi.ski.mskcc.org
   Cellular Biochemistry and Biophysics Program, Rockefeller Research
   Laboratories, Memorial Sloan-Kettering Cancer Center, 1275 York
   Avenue, Box 251,New York, NY 10021.
   
History

   Written (Jan 2001) - Bernd Jagla
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
