EMBOSS: restrict

| ## EMBOSS: restrict

# Program restrict

## Function

Finds restriction enzyme cleavage sites

## Description

Restrict uses the REBASE database of restriction enzymes to predict cut sites in a DNA sequence. The program allows you to select a range of cuts, whether the DNA is circular, whether IUB ambiguity codes are used, whether blunt or sticky ends or both are reported. You may also force the reporting of single cleavage sites.

## Usage

Here is a sample session with restrict.

    % restrict
    Finds restriction enzyme cleavage sites
    Input sequence(s): embl:hsfau
    Minimum recognition site length [4]:
    Comma separated enzyme list [all]:
    Output file [hsfau.restrict]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -sitelen            integer    Minimum recognition site length
       -enzymes            string     The name 'all' reads in all enzyme names
                                      from the REBASE database. You can specify
                                      enzymes by giving their names with commas
                                      between then, such as:
                                      'HincII,hinfI,ppiI,hindiii'.
                                      The case of the names is not important. You
                                      can specify a file of enzyme names to read
                                      in by giving the name of the file holding
                                      the enzyme names with a '@' character in
                                      front of it, for example, '@enz.list'.
                                      Blank lines and lines starting with a hash
                                      character or '!' are ignored and all other
                                      lines are concatenated together with a comma
                                      character ',' and then treated as the list
                                      of enzymes to search for.
                                      An example of a file of enzyme names is:
                                      ! my enzymes
                                      HincII, ppiII
                                      ! other enzymes
                                      hindiii
                                      HinfI
                                      PpiI
      [-outfile]           report     (no help text) report value

       Optional qualifiers: (none)
       Advanced qualifiers:
       -min                integer    Minimum cuts per RE
       -max                integer    Maximum cuts per RE
       -single             bool       Force single site only cuts
       -[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
       -[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
-sitelen | Minimum recognition site length | Integer from 2 to 20 | 4
-enzymes | The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'. The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'. Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI | Any string is accepted | all
[-outfile] (Parameter 2) | (no help text) report value | Report file |
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
-[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
-[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

The input sequence can be one or more DNA sequences.

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default restrict writes a 'table' report file.

The output from restrict 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. The program also reports isoschizomers and enzymes having the same recognition sequence but different cut sites.

Here is part of a sample output:

    ########################################
    # Program: restrict
    # Rundate: Mon Feb 11 13:46:44 2002
    # Report_file: hsfau.restrict
    ########################################

    #=======================================
    #
    # Sequence: HSFAU     from: 1   to: 518
    # HitCount: 214
    #
    # Minimum cuts per enzyme: 1
    # Maximum cuts per enzyme: 2000000000
    # Minimum length of recognition site: 4
    # Blunt ends allowed
    # Sticky ends allowed
    # DNA is linear
    # Ambiguities allowed
    #
    #
    #=======================================

    USA               Start     End   Score Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
    HSFAU                 3       6   0.000 MnlI        CCTC             13     12   .         .
    HSFAU                 9      14   0.000 Hpy188III   TCNNGA           10     12   .         .
    HSFAU                11      14   0.000 TaqI        TCGA             11     13   .         .
    HSFAU                13      17   0.000 HinfI       GANTC            13     16   .         .
    HSFAU                17      21   0.000 MlyI        GAGTC            7      7   .         .
    HSFAU                17      21   0.000 PleI        GAGTC            7      8   .         .
    HSFAU                24      27   0.000 AccII       CGCG             25     25   .         .
    HSFAU                24      28   0.000 MboII       GAAGA            12     11   .         .
    HSFAU                28      31   0.000 AciI        CCGC             25     27   .         .

    etc.

    HSFAU               437     443   0.000 DraII       RGGNCCY          438    441   .         .
    HSFAU               438     442   0.000 AspS9I      GGNCC            438    441   .         .
    HSFAU               438     443   0.000 BscBI       GGNNCC           440    440   .         .
    HSFAU               438     441   0.000 BshFI       GGCC             439    439   .         .
    HSFAU               438     441   0.000 CviJI       RGCY             439    439   .         .
    HSFAU               454     459   0.000 AflII       CTTAAG           454    458   .         .
    HSFAU               454     459   0.000 SmlI        CTYRAG           454    458   .         .
    HSFAU               455     458   0.000 MseI        TTAA             455    457   .         .
    HSFAU               468     471   0.000 Sse9I       AATT             467    471   .         .
    HSFAU               474     477   0.000 CviJI       RGCY             475    475   .         .
    HSFAU               492     495   0.000 CviJI       RGCY             493    493   .         .
    HSFAU               497     501   0.000 BstDEI      CTNAG            497    500   .         .

    #---------------------------------------
    #---------------------------------------

## 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

Output file size is related to the size of the recognition site and the maximum number of allowed cutting positions. Setting the site length to six and restricting the cuts to two is a common choice of parameters. The size of the output can sometimes be reduced by specifying the -noambiguity switch.

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

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

## Warnings

The program will warn you if a protein sequence is given.

## Diagnostic Error Messages

## Exit status

It exits with status 0 unless an error is reported.

## Known bugs

## 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
restover | Finds restriction enzymes that produce a specific overhang
showseq | Display a sequence with features, translation etc
silent | Silent mutation restriction enzyme scan

## Author(s)

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

## History

Completed 16th April 1999

## Target users

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

## Comments