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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
Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-seqcomp] string Overlap sequence (Any string is accepted) [-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 data file (optional) -min integer  Minimum cuts per RE (Integer from 1 to 1000) -max integer  Maximum cuts per RE (Integer up to 2000000000) -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. 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
|Standard (Mandatory) qualifiers||Allowed values||Default|
|Nucleotide sequence(s) filename and optional format, or reference (input USA)||Readable sequence(s)||Required|
|Overlap sequence||Any string is accepted||An empty string is accepted|
|Output file name||Output file||<*>.restover|
|Additional (Optional) qualifiers||Allowed values||Default|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
|-datafile||Restriction enzyme data file (optional)||Data file||File in the data file path|
|-mfile||Restriction enzyme data file (optional)||Data file||Emethylsites.dat|
|-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|
|-methylation||If this is set then RE recognition sites will not match methylated bases.||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|
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  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  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:P62861" FT /db_xref="HGNC:3597" FT /db_xref="HSSP:1GJZ" FT /db_xref="InterPro:IPR006846" FT /db_xref="UniProtKB/Swiss-Prot:P35544" 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
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.
|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|