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Restriction Cloning & Plasmids

Linear and Circular Restriction-Digest Mapping Workbench

Turn entered interbase cut coordinates into exact fragment ledgers for linear or circular molecules and reconcile enzyme set A, set B and their combined double digest.

Biology · experimental measurements

Keep topology, coordinate convention, coincident sites and single-versus-combined digests explicit without pretending to scan an enzyme database or predict laboratory completion.

Private calculations in your browser · explicit inputs and model boundaries
Example preview · Linear single digestSelected digest fragment lengths
Fragment 12,350 bp
Fragment 21,400 bp
Fragment 31,250 bp

Bars show every set-A fragment from largest to smallest. Their exact sum is 5,000 bp, equal to the entered molecule length.

  1. 1EnterProvide the known values
  2. 2CalculateResults update automatically
  3. 3VerifyReview the details and units
Try an example

Enter values in bp.

One row per cut: group A or B, site/enzyme label, interbase position. Example: A,EcoRI,1250

Calculation result

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Enter valid values to see the result.

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Understand the relationship

The reasoning behind the result

Interbase coordinates identify breaks

Position zero is the boundary before the first displayed base. A cut at position x divides the molecule after x bases in the linear convention.

Linear endpoints are not entered as cuts; circular position zero is a valid origin boundary.

Topology changes the fragment count

linear: fragments = unique cuts + 1; circular: fragments = unique cuts when cuts > 0

A linear molecule retains two physical ends. A circular molecule has no ends, so one cut linearizes it into one full-length fragment.

The circular ledger includes the fragment that crosses the chosen coordinate origin.

A double digest uses the union of breaks

The combined digest takes every unique coordinate from groups A and B. Coincident enzyme sites remain separately labelled in the input ledger but create one physical break.

Single-digest summaries make it possible to reconcile which added site split which fragment.

A coordinate model is not an enzyme simulation

Recognition sequences, strand-specific offsets, methylation, star activity and partial digestion are not inferred. The visitor supplies cut coordinates already justified for the molecule and conditions.

Gel bands can merge when fragments have similar sizes; this arithmetic ledger does not predict observed band resolution or intensity.

Follow the numbers

Digest a 5,000 bp linear molecule

  1. Declare a linear 5,000 bp molecule.
  2. Enter set-A cuts at interbase coordinates 1,250 and 3,600.
  3. Sort the boundaries as 0, 1,250, 3,600 and 5,000.
  4. Take consecutive differences: 1,250 bp, 2,350 bp and 1,400 bp.
  5. Confirm the fragments sum to the original 5,000 bp molecule.

The fragment ledger follows the supplied complete-cut coordinates; enzyme recognition and laboratory completion remain external.

Quick guide

How to use this calculator

  1. Declare whether the entered molecule is linear or circular and enter its exact length.
  2. Record every known cut as group A or B, a descriptive label and an interbase coordinate.
  3. Choose the single or combined digest view and reconcile fragment lengths to the complete molecule length.

Calculation method

Calculation and interpretation

Keep topology, coordinate convention, coincident sites and single-versus-combined digests explicit without pretending to scan an enzyme database or predict laboratory completion.

Linear fragments are consecutive differences across [0, sorted unique cuts, L]. Circular fragments are cyclic differences between sorted unique cuts, including the last-to-first distance across the origin.

Worked example

Digest a 5,000 bp linear molecule

The fragment ledger follows the supplied complete-cut coordinates; enzyme recognition and laboratory completion remain external.

Linear fragments are consecutive differences across [0, sorted unique cuts, L]. Circular fragments are cyclic differences between sorted unique cuts, including the last-to-first distance across the origin.

Supported inputs

Precision and limits

Entered coordinates

The workbench does not scan DNA sequence or provide a maintained restriction-enzyme recognition database.

Complete digest arithmetic

Every selected site is treated as cut; partial digestion, star activity, methylation and reaction efficiency are excluded.

Interbase convention

Linear cuts must be inside the molecule; circular cuts may include coordinate zero but not the molecule length.

Coincident cuts

Multiple labels at one coordinate create one physical break in the combined fragment calculation.

No gel prediction

Fragment order and exact sizes are reported; migration, band merging, staining and detectability are not inferred.

Computational support

Whole molecule lengths from 2 through 100,000,000 bp and up to 200 labelled cut rows are supported.

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