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: 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 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
restoverFinds restriction enzymes that produce a specific overhang
showseqDisplay a sequence with features, translation etc
silentSilent 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