Molecular biology software for restriction profiling and restriction digest simulation

Restriction Analyzer will accept an input DNA sequence and produce a comprehensive report of the restriction enzymes that will cleave the sequence.

It produces a variety of outputs including restriction enzyme maps and theoretical digests presented as restriction fragment list and a simulated electropherogram. Thus the output of the program is an online restriction profile of a DNA sequence.

Restriction digest is a method that uses several restriction enzymes to detect variations from the expected digestion patterns of DNA sequences. Restriction Analyzer is a restriction profiles online program and restriction digest simulator.

Restriction Analyzer provides an online restriction site analysis and can also be seen as a restriction fragment calculator. As a result, the user will get restriction enzymes patterns and DNA fragment size calculation.

Restriction Analyzer provides comprehensive restriction analysis of a DNA molecule

Restriction digests are mixtures of DNA fragments produced by the reaction of DNA and a restriction enzyme, an enzyme that cuts at specific base sequences. These enzymes are used for the creation of genetic maps prior to sequencing.

To perform restriction mapping of plasmid DNA and find restriction enzyme sites, use Restriction Analyzer.

Restriction Analyzer can also display restriction enzymes sequence and perform restrictase screen and restriction digestion.

In summary, Restriction Analyzer is a valuable molecular biology software, a web app, also molecular cloning software tool which enables the user to find restriction sites (restriction endonuclease recognition patterns) and is an important modern alternative to older programs like NEBcutter, RestrictionMapper, or WebCutter. In other words, Restriction Analyzer is a restriction patterns online utility.

Restriction Analyzer@molbiotools.com

genetic code genetic code useful linx send feedback user guide
Display standard genetic code IUPAC ambiguous/degenerate positions 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

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genetic code

IUPAC AMBIGUITY CODE

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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