Restriction Fragment Length Calculator

Restriction Fragment Length Calculator | Online Free Tool | Elysia Tools

Tool usage guide

Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Category: Education
Input types: select, number, text
Output type: json
Sample coverage: 4
API ready: Yes

Overview

The Restriction Fragment Length Calculator estimates DNA fragment sizes after restriction digestion. Choose circular plasmid or linear DNA, then enter exact cut positions for fragment lengths or provide a cut-site count for an average estimate.

When to use

Predict fragment sizes for a circular plasmid single or double digest.
Calculate the fragments produced when linear DNA is cut at known coordinates.
Estimate fragment count and average size when only the number of restriction sites is known.

How it works

1Select the substrate topology: circular plasmid or linear DNA.
2Choose exact cut positions or cut-site count as the input mode.
3Enter the substrate length in base pairs and provide the required positions or site count.
4The calculator returns fragment sizes, fragment count, mean length, minimum and maximum lengths, and the conserved total length.

Use cases

Planning plasmid restriction digests and checking expected band sizes.
Interpreting restriction maps for linear DNA or PCR products.
Comparing predicted fragment sizes with agarose gel observations for educational or experimental planning.

Examples

1. pUC19 circular double digest

Molecular biology student

Background

A 2686 bp circular pUC19 plasmid has restriction sites at positions 1000 and 2000.

Problem

Determine the fragment sizes expected from the two cuts.

How to use

Select Circular plasmid and Cut positions, enter 2686 as the substrate length, and enter 1000, 2000 as the cut positions.

Topology: circular; input mode: positions; substrate length: 2686 bp; cut positions: 1000, 2000.

Outcome

The calculator returns 2 fragments of 1000 bp and 1686 bp, with a conserved total of 2686 bp and a mean length of 1343 bp.

2. Linear PCR product digest

Teaching laboratory instructor

Background

A 5000 bp linear PCR product is cut at internal positions 1500 and 3000.

Problem

Calculate the three DNA fragments produced by the two cuts.

How to use

Select Linear DNA and Cut positions, enter 5000 as the substrate length, and enter 1500, 3000 as the cut positions.

FAQ

How many fragments result from n cuts?

A circular substrate produces n fragments, while linear DNA produces n+1 fragments.

How do I enter exact cut positions?

Enter unique, comma-separated coordinates counted from base 1, such as 1000, 2000.

What does the cut-site count mode calculate?

It calculates the expected fragment count and average fragment length assuming an even distribution of cut sites.

Does the calculator account for circular wrap-around?

Yes. For circular substrates, it includes the fragment that crosses the origin.

What are the expected frequencies of four- and six-base recognition sites?

In random DNA, a four-base site is expected about once every 256 bp and a six-base site about once every 4096 bp.

Topology: linear; input mode: positions; substrate length: 5000 bp; cut positions: 1500, 3000.

Run this tool

Examples that match this tool

Continue with connected tools and hubs

Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Overview

When to use

How it works

Use cases

Examples

1. pUC19 circular double digest

2. Linear PCR product digest

FAQ

Web Image Processing Python Samples

Length Distance Samples

Length Unit Samples

Android Image Processing Java Samples

Amino Acid Composition Analyzer

Bottleneck Effect Simulator (heterozygosity loss)

Data Boundary Processor

Protein Molecular Weight Calculator (from Sequence)

3. Average fragment estimate from site count