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restover |
Function
Find restriction enzymes producing specific overhangDescription
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 It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.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/
restover takes a specified sequence and a short sequence of a cut-site overhang and searches the REBASE database for matching enzymes that create the desired overhang sequence when they cut the input sequence.
Usage
Here is a sample session with restover
% restover Find restriction enzymes producing specific overhang Input sequence(s): tembl:hsfau Overlap sequence: cg Output file [hsfau.restover]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
[-seqcomp] string Overlap sequence
[-outfile] outfile Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-datafile datafile Alternative RE data file
-min integer Minimum cuts per RE
-max integer Maximum cuts per RE
-single boolean Force single site only cuts
-threeprime boolean Use 3' overhang e.g. BamHI has CTAG as a 5'
overhang, and ApaI has CCGG as 3' overhang.
-[no]blunt boolean Allow blunt end cutters
-[no]sticky boolean Allow sticky end cutters
-[no]ambiguity boolean Allow ambiguous matches
-plasmid boolean Allow circular DNA
-[no]commercial boolean Only enzymes with suppliers
-html boolean Create HTML output
-[no]limit boolean Limits reports to one isoschizomer
-alphabetic boolean Sort output alphabetically
-fragments boolean Show fragment lengths
-name boolean Show sequence name
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 standard output
-filter boolean Read standard input, write 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. 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| [-seqcomp] (Parameter 2) |
Overlap sequence | Any string is accepted | An empty string is accepted |
| [-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.restover |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -datafile | Alternative RE data file | Data file | File in the data file path |
| -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 | Boolean value Yes/No | No |
| -threeprime | 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 | Allow blunt end cutters | Boolean value Yes/No | Yes |
| -[no]sticky | Allow sticky end cutters | Boolean value Yes/No | Yes |
| -[no]ambiguity | Allow ambiguous matches | Boolean value Yes/No | Yes |
| -plasmid | Allow circular DNA | Boolean value Yes/No | No |
| -[no]commercial | Only enzymes with suppliers | Boolean value Yes/No | Yes |
| -html | Create HTML output | Boolean value Yes/No | No |
| -[no]limit | Limits reports to one isoschizomer | Boolean value Yes/No | Yes |
| -alphabetic | Sort output alphabetically | Boolean value Yes/No | No |
| -fragments | Show fragment lengths | Boolean value Yes/No | No |
| -name | Show sequence name | Boolean value Yes/No | No |
Input file format
restover reads in a normal nucleic acid sequence USA.Input files for usage example
'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:hsfau
ID HSFAU standard; RNA; HUM; 518 BP.
XX
AC X65923;
XX
SV X65923.1
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 23-SEP-1993 (Rel. 37, Last updated, Version 10)
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; Primates; Catarrhini; Hominidae; 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 MEDLINE; 93368957.
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 sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8:2537-2546(1993).
XX
DR SWISS-PROT; P35544; UBIM_HUMAN.
DR SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /chromosome="11q"
FT /db_xref="taxon:9606"
FT /organism="Homo sapiens"
FT /tissue_type="placenta"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /map="13"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /db_xref="SWISS-PROT:P35544"
FT /db_xref="SWISS-PROT:Q05472"
FT /gene="fau"
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
//
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Output file format
Output files for usage example
File: hsfau.restover
# Restrict of HSFAU 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 iin 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 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 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
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| recoder | Remove restriction sites but maintain same translation |
| redata | Search REBASE for enzyme name, references, suppliers etc |
| remap | Display sequence with restriction sites, translation etc |
| restrict | Finds restriction enzyme cleavage sites |
| showseq | Display a sequence with features, translation etc |
| silent | Silent mutation restriction enzyme scan |
Author(s)
Bernd Jagla (bernd © golgi.ski.mskcc.org)Cellular Biochemistry and Biophysics Program, Rockefeller Research Laboratories, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 251,New York, NY 10021.