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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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

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 nameDescription
recoderRemove restriction sites but maintain the same translation
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent 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.

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