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
Input sequence [stdin]: ecrrnbz
Begin at [1]: 
End at [7508]: 
Minimum cuts [1]:
Maximum cuts [2]: 2
Minimum recognition site length [4]: 6
Output file [stdout]: ecrrnbz.out

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]           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
   -[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
   -[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
   -datafile           string     Alternative RE data file

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) Output file name Output file <sequence>.restrict

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

-[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

-datafile Alternative RE data file Any string is accepted An empty string is accepted

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)	Output file name	Output file	<sequence>.restrict
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
-[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
-datafile	Alternative RE data file	Any string is accepted	An empty string is accepted

Input file format

The input sequence can be one or more DNA sequences.

Output file format

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:

# Restrict of ECRRNBZ from 1 to 7508
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2
# Minimum length of recognition site: 6
# Blunt ends allowed
# Sticky ends allowed
# DNA is linear
# Ambiguities allowed
# Number of hits: 442
#
# Base Number   Enzyme          Site            3'      5'      [3'     5']
        1       Nsp29132II      GGATCC          1       5
        1       BspAAIII        GGATCC          1       5
        1       AccEBI          GGATCC          1       5
        1       Bsp4009I        GGATCC          1       5
        1       BstI            GGATCC          1       5
        1       AliI            GGATCC          1       5
        1       SolI            GGATCC          1       5
        1       Mlu23I          GGATCC          1       5
        1       ApaCI           GGATCC          1       5
        1       BnaI            GGATCC          1       5
        1       SurI            GGATCC          1       5
        1       OkrAI           GGATCC          1       5
        1       NspSAIV         GGATCC          1       5
        1       RspLKII         GGATCC          1       5
        1       BamHI           GGATCC          1       5
        1       Bce751I         GGATCC          1       5
        17      BssSI           CACGAG          17      21
        17      BsiI            CACGAG          17      21
        17      Bst2BI          CACGAG          17      21
        24      NsbI            TGCGCA          26      26
        24      AviII           TGCGCA          26      26
        24      MstI            TGCGCA          26      26
        24      Acc16I          TGCGCA          26      26
        24      PamI            TGCGCA          26      26
        24      AosI            TGCGCA          26      26
        24      FspI            TGCGCA          26      26
        24      FdiII           TGCGCA          26      26

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

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

Program name	Description
chaos	Create a chaos game representation plot for a sequence
cpgplot	Plot CpG rich areas
cpgreport	Reports all CpG rich regions
diffseq	Find differences (SNPs) between nearly identical sequences
dotmatcher	Displays a thresholded dotplot of two sequences
dotpath	Displays a non-overlapping wordmatch dotplot of two sequences
dottup	Displays a wordmatch dotplot of two sequences
einverted	Finds DNA inverted repeats
equicktandem	Finds tandem repeats
etandem	Looks for tandem repeats in a nucleotide sequence
isochore	Plots isochores in large DNA sequences
newcpgreport	Report CpG rich areas
newcpgseek	Reports CpG rich regions
palindrome	Looks for inverted repeats in a nucleotide sequence
polydot	Displays all-against-all dotplots of a set of sequences
rebaseextract	Extract data from REBASE
redata	Search REBASE for enzyme name, references, suppliers etc
remap	Display a sequence with restriction cut sites, translation etc
showseq	Display a sequence with features, translation etc
silent	Silent mutation RE scan
tfscan	Scans DNA sequences for transcription factors

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.