Restriction Profiling of DNA

online tool for restriction analysis of two sequences

compare restriction profiles

restriction digest with gel electrophoresis simulation

compare restriction patterns online utility

restriction enzymes patterns dna fragment size calculation

web app to compare restriction sites

restriction profiles comparison online tool

restriction mapping of plasmid dna

restriction analysis molecular biology software molecular biology web app molecular cloning software tools find restriction sites analyse restriction sites analyze restriction sites restriction enzyme restriction mapping NEB cutter

DNA ladder

View Example

DNA SEQUENCE INPUT

A
linear circular

Name:

Length:

B
linear circular

Name:

Length:

RESTRICTION SITES

Present in A, absent in B

Present in B, absent in A

Present in both, different counts

×

RESTRICTION FRAGMENTS

Selected enzymes: Ctrl+click for multiple selection (more than 3 enzymes)


DISCERNING CLEAVAGE SUGGESTIONS

SETTINGS

Restriction sites

(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

Restriction fragments

DNA source genotype

dam+ dam-
dcm+ dcm-

Discerning cleavage suggestions

Target fragment range

-

Minimum fragment size difference

%

Maximum number of enzymes to combine

Max. 4
Prioritize these enzymes:
Apply & Analyze

info@molbiotools.com


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 Comparator application contains a list of all commercially available restriction enzymes. From these 543 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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TARGET FRAGMENT RANGE

For a cleavage pattern to be suggested as discerning, at least one fragment within the target range must be produced by such cleavage in at least one sequence.

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MINIMUM FRAGMENT SIZE DIFFERENCE

For a cleavage pattern to be suggested as discerning, at least one fragment within the target range must differ from each fragment from the other sequence by at least the entered number of percents of the size of that fragment.

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