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Restriction Analyzer@molbiotools.com

genetic code genetic code compatible ends useful linx send feedback user guide
Display standard genetic code IUPAC ambiguous/degenerate positions Enzymes producing compatible ends Useful links Send feedback! User guide

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DNA SEQUENCE INPUT & SETTINGS

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×
View Example

DNA form:

linear circular

Name:

Length:

Restriction sites selection

(display current list)
pre-selected commonly used enzymes
criteria-based selection
user-provided list

Enter the restriction enzyme list

Load the restriction enzyme list from a file


ignore sites blocked by methylation
Apply & Analyze

RESTRICTION SITES OVERVIEW

Present

Absent

Unique

RESTRICTION FRAGMENTS

DNA source genotype:

dam+ dam- dcm+ dcm-
Sites selected: Ctrl+click for multiple selection (more than 3 enzymes)

ANNOTATED SEQUENCE


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DISCLAIMER: This free software comes without any warranty. The author of the software bears no responsibility for any loss or damage that may arise from its use for any purpose.

COMMONLY USED ENZYMES

This is a manual selection of the most frequently used enzymes, typically those whose recognition sites are present in the multiple cloning sites region of commonly used plasmid vectors plus some other enzymes traditionally used for restriction analysis and molecular cloning.

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CRITERIA-BASED SELECTION

The Restriction Analyzer application contains a list of all commercially available restriction enzymes. From these 549 enzymes, you can select a subset based on the length of recognition sites or a presence of ambiguous positions in them.

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USER-PROVIDED LIST

If a specific set of restriction enzymes is to be used in the analyses, one can either enter the list (paste it in the text area in the "Enter the restriction enzyme list" dialog) or load a list of enzymes provided as a plain text file with one restriction enzyme name per line, for example:
BamHI
EcoRI
HindIII
etc.

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DNA SOURCE GENOTYPE

Plasmid DNA isolated from E. coli is methylated on Dam and Dcm sites unless a dam-/dcm- strain has been used. DNA obtained with PCR amplification is rid of all methylation so "dam- " and "dcm- " should be checked in such cases.

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STANDARD GENETIC CODE

×
genetic code

IUPAC AMBIGUITY CODE

×
Symbol Bases represented Complement
R A, G Y
Y C, T R
K G, T M
M A, C K
S C, G S
W A, T W
B C, G, T V
D A, G, T H
H A, C, T D
V A, C, G B
N A, C, G, T N

COMPATIBLE ENDS

×
Overhang Enzymes
N│G A T C N N C T A G│N BamHI, BglII
N│A A T T N N T T A A│N EcoRI, MfeI (MunI)
N│T C G A N N A G C T│N SalI, XhoI
N│C T A G N N G A T C│N AvrII (XmaJI), NheI, SpeI (BcuI), XbaI
N T G C A│N N│A C G T N NsiI (Mph1103I), PstI
N│G T A C N N C A T G│N Acc65I (Asp718I), BsiWI (Pfl23II), BsrGI (Bsp1407I)
N│C C G G N N G G C C│N AgeI (BshTI), BspEI (Kpn2I), XmaI (Cfr9I)
N│G G C C N N C C G G│N EagI (Eco52I), PspOMI (Bsp120I), NotI
N│C G C G N N G C G C│N AscI (SgsI), BssHII (PauI), MluI
N N│C G N N N N G C│N N AclI (Psp1406I), BstBI (Bsp119I), ClaI (Bsu15I), NarI
N N│T A N N N N A T│N N AseI (VspI), NdeI
N N A T│N N N N│T A N N PacI, PvuI
blunt ends AfeI (Eco47III), BsaBI (BseJI), DraI, EcoRV (Eco32I), Ecl136II, FspI (NsbI), HpaI (KspAI), MscI (MlsI), NaeI (PdiI), NruI (Bsp68I), PmeI (MssI), PmlI (Eco72I), PvuII, ScaI, SfoI (EheI), SmaI, SnaBI (Eco105I), SrfI, SspI, StuI (Eco147I), SwaI (SmiI), XmnI (PdmI), ZraI