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EMBOSS: 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]:
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] outfile Output file name 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 -[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 -datafile string Alternative RE data file |
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) |
Output file name | Output file | <sequence>.restrict |
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 |
-[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 |
-datafile | Alternative RE data file | Any string is accepted | An empty string is accepted |
# Restrict of HSFAU from 1 to 518 # # 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 # Number of hits: 208 # Base Number Enzyme Site 5' 3' [5' 3'] 3 MnlI CCTC 13 12 9 Hpy188III TCNNGA 10 12 11 TaqI TCGA 11 13 13 HinfI GANTC 13 16 17 MlyI GAGTC 7 7 17 PleI GAGTC 7 8 24 AccII CGCG 25 25 24 MboII GAAGA 12 11 28 AciI CCGC 25 27 30 AluI AGCT 31 31 30 CviJI RGCY 31 31 31 MwoI GCNNNNNNNGC 37 34 34 BscBI GGNNCC 36 36 34 BsmFI GGGAC 48 52 35 AspS9I GGNCC 35 38 35 AvaII GGWCC 35 38 38 AciI CCGC 38 40 58 CviRI TGCA 59 59 59 BbvI GCAGC 71 75 59 Fnu4HI GCNGC 60 61 59 TseI GCWGC 59 62 61 AluI AGCT 62 62 61 CviJI RGCY 62 62 71 AciI CCGC 71 73 71 Bsc4I CCNNNNNNNGG 77 74 72 AccII CGCG 73 73 73 AspLEI GCGC 75 73
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.
Program name | Description |
---|---|
chaos | Create a chaos game representation plot for a sequence |
cpgplot | Plot CpG rich areas |
cpgreport | Reports all CpG rich regions |
diffseq | Find differences (SNPs) between nearly identical sequences |
dotmatcher | Displays a thresholded dotplot of two sequences |
dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
einverted | Finds DNA inverted repeats |
equicktandem | Finds tandem repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
isochore | Plots isochores in large DNA sequences |
newcpgreport | Report CpG rich areas |
newcpgseek | Reports CpG rich regions |
palindrome | Looks for inverted repeats in a nucleotide sequence |
polydot | Displays all-against-all dotplots of a set of sequences |
rebaseextract | Extract data from REBASE |
redata | Search REBASE for enzyme name, references, suppliers etc |
remap | Display a sequence with restriction cut sites, translation etc |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |
tfscan | Scans DNA sequences for transcription factors |