EMBOSS: restover

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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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