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DNA Sequence Tools
Text and Data Tools
Calculators

DNA Sequence Tools

DNA Sequence Editor (WebDSV )

Basic molecular biology app to create, edit and analyze DNA sequences, mark and visualize sequence features, and generate plasmid maps. With WebDSV you can analyze restriction sites, perform in silico molecular cloning, and design PCR primers. No registration is needed. All processing runs locally, no data are sent over the internet.

PCR Primer Inspector

Calculate melting temperatures of DNA oligonucleotides. Analyze potential primer dimers. Batch processing of multiple sequences.

Restriction Analyzer

Carry out in silico restriction analysis online. Quickly find absent and unique sites. Tabular and graphical output. Analyze restriction fragments. Simulate a gel electrophoresis.

Restriction Comparator

Carry out parallel in silico restriction analysis online. Compare two sequences side by side. Find distinguishing restriction sites. Visualize restriction patterns.

Silent Mutator

In silico silent mutagenesis online tool. Introduce new restriction sites without changing the encoded amino acid sequence. Supports all commercially available restriction enzymes. Supports all genetic codes. Unlimited sequence length.

Random Sequence Generator

Generate random DNA, RNA or protein sequences. Based on the Mersenne Twister algorithm. No unwanted repeats are generated even in very long sequences. Can be used for calculations of DNA, RNA and protein molecular weights and for string reverse and complement transformations (also with user-provided sequences).

Text and Data Tools

Target Text Extractor

Find and extract or remove target text patterns. Extract text between words. Extract words that begin with specific characters. Extract gene symbols from complex annotations. Online regular expression searching and match-extracting tool.

Multiple List Comparator

Compare data lists to find shared items. Find intersections among large data sets. Tabular data import (optional). Venn diagram drawing tool (png and svg export). Compare up to 100 lists.

List Operations

Perform set operations on data lists (union, intersection, subtraction). Remove duplicate items. Sort, reverse, or shuffle a list.

Table Operations

Remove rows or columns by number, order patterns, or specific content such as numeric value ranges or character patterns. Modify cell contents by removing, replacing, prefixing or appending characters. Rearrange tables by moving columns under each other. Easy transfer of data from and back into a spreadsheet software.

Two-table Operations

Extract or remove table rows with a selection list. Extract table rows by reference columns match. Align two tables.

Random Gene Set Generator

Generate random gene lists of defined length. Challenge GSEA results with random gene sets to estimate true significance of enrichments found with real data.

Calculators

DNA Calculator

Calculate basic chemical properties of a DNA or RNA molecule. Calculate concentration from 260 nm absorbance. Calculate molarity, mass or volume. Calculate base-pair molarity of dsDNA solutions.

Chemical Calculator

Calculate molarity, mass or volume. Calculate molarity from percentual concentration. Calculate dilution of stock solutions.

Buffer Calculator

With this tool you can estimate the pH value of a buffer solution with Henderson-Hasselbalch equation. Also, a list of pKa values of common buffers is provided.

Centrifugation

Experiment protocols may contain both relative centrifugation force (RCF) and revolutions per minute (RPM) values in centrifugation parameter specifications. This tool allows you to convert between RCF and RPM.

Combinatorics

How many different selections of items from a collection can you get? How many times a set of items can be rearranged? Use this tool to calculate numbers of combinations and permutations.

Probabilities

Calculate probabilities of random events following Poisson, binomial, hypergeometric, geometric or negative binomial distribution.

Molbiotools molecular biology free web apps molecular cloning help free online software tools and information resources for molecular cloning web browser-based applications that work the same on Windows, Mac and Linux systems free online molecular cloning software for molecular cloning

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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.