EMBOSS: restover

| restover

## Wiki

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## Function

Find restriction enzymes producing a specific overhang

## Description

restover identifies restriction enzymes from the REBASE database that create the specified overhang sequence when they cut the input nucleotide sequence(s). It writes an output file which shows the base number, restriction enzyme name, recognition site and cut positions. There are several options to control exactly what sites are reported and the format of the output file. Optionally, output in HTML may be generated.

## Usage

Here is a sample session with restover

    % restover
    Find restriction enzymes producing a specific overhang
    Input nucleotide sequence(s): tembl:x65923
    Overlap sequence: cg
    Output file [x65923.restover]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Find restriction enzymes producing a specific overhang
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                      format, or reference (input USA)
      [-seqcomp]           string     Overlap sequence (Any string)
      [-outfile]           outfile    [*.restover] Output file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -datafile           datafile   Restriction enzyme data file (optional)
       -mfile              datafile   [Emethylsites.dat] Restriction enzyme
                                      methylation data file
       -min                integer    [1] Minimum cuts per RE (Integer from 1 to
                                      1000)
       -max                integer    [2000000000] Maximum cuts per RE (Any
                                      integer value)
       -single             boolean    [N] Force single site only cuts
       -threeprime         boolean    [N] Use 3' overhang e.g. BamHI has CTAG as a
                                      5' overhang, and ApaI has CCGG as 3'
                                      overhang.
       -[no]blunt          boolean    [Y] Allow blunt end cutters
       -[no]sticky         boolean    [Y] Allow sticky end cutters
       -[no]ambiguity      boolean    [Y] Allow ambiguous matches
       -plasmid            boolean    [N] Allow circular DNA
       -methylation        boolean    [N] If this is set then RE recognition sites
                                      will not match methylated bases.
       -[no]commercial     boolean    [Y] Only enzymes with suppliers
       -html               boolean    [N] Create HTML output
       -[no]limit          boolean    [Y] Limits reports to one isoschizomer
       -alphabetic         boolean    [N] Sort output alphabetically
       -fragments          boolean    [N] Show fragment lengths

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -scircular1         boolean    Sequence is circular
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -odirectory3        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-seqcomp] (Parameter 2) | string | Overlap sequence | Any string |
[-outfile] (Parameter 3) | outfile | Output file name | Output file | <*>.restover
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-datafile | datafile | Restriction enzyme data file (optional) | Data file | File in the data file path
-mfile | datafile | Restriction enzyme methylation data file | Data file | Emethylsites.dat
-min | integer | Minimum cuts per RE | Integer from 1 to 1000 | 1
-max | integer | Maximum cuts per RE | Any integer value | 2000000000
-single | boolean | Force single site only cuts | Boolean value Yes/No | No
-threeprime | boolean | Use 3' overhang e.g. BamHI has CTAG as a 5' overhang, and ApaI has CCGG as 3' overhang. | Boolean value Yes/No | No
-[no]blunt | boolean | Allow blunt end cutters | Boolean value Yes/No | Yes
-[no]sticky | boolean | Allow sticky end cutters | Boolean value Yes/No | Yes
-[no]ambiguity | boolean | Allow ambiguous matches | Boolean value Yes/No | Yes
-plasmid | boolean | Allow circular DNA | Boolean value Yes/No | No
-methylation | boolean | If this is set then RE recognition sites will not match methylated bases. | Boolean value Yes/No | No
-[no]commercial | boolean | Only enzymes with suppliers | Boolean value Yes/No | Yes
-html | boolean | Create HTML output | Boolean value Yes/No | No
-[no]limit | boolean | Limits reports to one isoschizomer | Boolean value Yes/No | Yes
-alphabetic | boolean | Sort output alphabetically | Boolean value Yes/No | No
-fragments | boolean | Show fragment lengths | Boolean value Yes/No | No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory3 -odirectory_outfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

restover reads in one or more nucleotide sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### Input files for usage example

'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:x65923

    ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
    XX
    AC   X65923;
    XX
    DT   13-MAY-1992 (Rel. 31, Created)
    DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
    XX
    DE   H.sapiens fau mRNA
    XX
    KW   fau gene.
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
    OC   Homo.
    XX
    RN   [1]
    RP   1-518
    RA   Michiels L.M.R.;
    RT   ;
    RL   Submitted (29-APR-1992) to the INSDC.
    RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
    RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
    XX
    RN   [2]
    RP   1-518
    RX   PUBMED; 8395683.
    RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
    RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
    RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
    RL   Oncogene 8(9):2537-2546(1993).
    XX
    DR   Ensembl-Gn; ENSG00000149806; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000279259; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000434372; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000525297; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000526555; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000527548; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000529259; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000529639; Homo_sapiens.
    DR   Ensembl-Tr; ENST00000531743; Homo_sapiens.
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..518
    FT                   /organism="Homo sapiens"
    FT                   /chromosome="11q"
    FT                   /map="13"
    FT                   /mol_type="mRNA"
    FT                   /clone_lib="cDNA"
    FT                   /clone="pUIA 631"
    FT                   /tissue_type="placenta"
    FT                   /db_xref="taxon:9606"
    FT   misc_feature    57..278
    FT                   /note="ubiquitin like part"
    FT   CDS             57..458
    FT                   /gene="fau"
    FT                   /db_xref="GDB:135476"
    FT                   /db_xref="GOA:P35544"
    FT                   /db_xref="GOA:P62861"
    FT                   /db_xref="H-InvDB:HIT000322806.14"
    FT                   /db_xref="HGNC:3597"
    FT                   /db_xref="InterPro:IPR000626"
    FT                   /db_xref="InterPro:IPR006846"
    FT                   /db_xref="InterPro:IPR019954"
    FT                   /db_xref="InterPro:IPR019955"
    FT                   /db_xref="InterPro:IPR019956"
    FT                   /db_xref="PDB:2L7R"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
    FT                   /protein_id="CAA46716.1"
    FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
    FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
    FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
    FT   misc_feature    98..102
    FT                   /note="nucleolar localization signal"
    FT   misc_feature    279..458
    FT                   /note="S30 part"
    FT   polyA_signal    484..489
    FT   polyA_site      509
    XX
    SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
         ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
         agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
         cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
         tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
         tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
         gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
         agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
         cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
         tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
    //

## Output file format

### Output files for usage example

### File: x65923.restover

    # Restrict of X65923 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: 54
    # Base Number	Enzyme		Site		5'	3'	[5'	3']
    	11	TaqI            TCGA            11	13
    	28	AciI            CCGC            25	27
    	38	AciI            CCGC            38	40
    	44	BceAI           ACGGC           25	27
    	71	AciI            CCGC            71	73
    	73	Hin6I           GCGC            73	75
    	94	TaqI            TCGA            94	96
    	103	HpaII           CCGG            103	105
    	162	HpaII           CCGG            162	164
    	190	Hin6I           GCGC            190	192
    	192	Hin6I           GCGC            192	194
    	225	BsrI            ACTGG           221	219
    	229	AciI            CCGC            226	228
    	263	AciI            CCGC            263	265
    	380	AciI            CCGC            377	379
    	383	AciI            CCGC            380	382
    	395	HpaII           CCGG            395	397
    	398	Hin6I           GCGC            398	400
    	408	AclI            AACGTT          409	411
    	409	MaeII           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

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

The EMBOSS REBASE restriction enzyme data files are stored in directory 'data/REBASE/*' under the EMBOSS installation directory.

These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager.

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

The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish.

The format of the file "embossre.equ" is
Enzyme-name Prototype-name

i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name.

## Notes

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/

Several criteria may be set to control what sites are reported: `-min`, `-max`, `-single` (minimum or maximum number of cuts, or single site cuts only. `-blunt` (enzymes which cut at the same position on the forward and reverse strands). `-sticky` (enzymes which cut at different positions on the forward and reverse strands, leaving an overhang). `-ambiguity` (enzymes which have one or more `N` ambiguity codes in their pattern). `-commercial` (enzymes with a commercial supplier). `-plasmid` (allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence).

By default, only one enzyme of any group of isoschizomers (enzymes that have the same recognition site and cut positions) is reported. This behaviour can be changed by specifying '-nolimit', in which case all isoschizomers are reported. The default behaviour uses the representative enzyme of an isoschizomer group (the prototype) which is specified in the EMBOSS data file `embossre.equ`. This file is generated from the REBASE database by running rebaseextract. You may edit this file to set your own preferred prototype,if you wish.

## References

None.

## Warnings

restover uses the EMBOSS REBASE restriction enzyme data files stored in directory `data/REBASE/*` under the EMBOSS installation directory. These files must first be set up using the program rebaseextract. Running rebaseextract may be the job of your system manager.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
recoder | Find restriction sites to remove (mutate) with no translation change
redata | Retrieve information from REBASE restriction enzyme database
remap | Display restriction enzyme binding sites in a nucleotide sequence
restrict | Report restriction enzyme cleavage sites in a nucleotide sequence
showseq | Display sequences with features in pretty format
silent | Find restriction sites to insert (mutate) with no translation change

## Author(s)

Bernd Jagla formerly at:
Cellular Biochemistry and Biophysics Program, Rockefeller Research Laboratories, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 251,New York, NY 10021.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## 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

None