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restover |
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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.
% 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
Find restriction enzymes producing a specific overhang
Version: EMBOSS:6.4.0.0
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
-sformat1 string Input sequence format
-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 |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -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 |
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.
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 EMBL/GenBank/DDBJ databases.
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 H-InvDB; HIT000322806.
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="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="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
//
|
# 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.
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:
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:
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.
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.
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.
| 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 | Displays sequences with features in pretty format |
| silent | Find restriction sites to insert (mutate) with no translation change |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.