Welcome to the GenomeWeb
Nucleic Acid General Sequence Analysis Analysis

Search for:

These are a collection of nucleic acid sequence analysis utilities.

[info] BCM Search Launcher
[info] Cutter - restriction mapping tool
[info] DNA Mutation Checker
[info] bend.it Server
[info] AG BIODV - MatInd, MatInspector, ConsInd, ConsInspector, GenomeInspector, ModelInspector
[info] Translation Utility
[info] Mutability - check sequences for potential Nonsense/Missense/Neutral mutations
[info] EnzFinder - A restriction engine search engine.
[info] MELTING: enthalpie, entropy and melting temperature
[info] A280/A260 calculator
[info] LabOnWeb

Detailed information on the above options

The Biology Workbench is a point and click WWW interface for an integrated set of programs and database searching tools that allow you to carry out sequence analysis without having to log into a remote computer site.

The service is free to non-commercial researchers (you just need to register). There is a comprehensive demonstration to help you get started.

BCM Search Launcher
The BCM Search Launcher provides

Other BCM Search and Analysis Services:

Cutter - restriction mapping tool
Webcutter is an on-line tool for restriction mapping nucleotide sequences. It features:

DNA Mutation Checker
DNA Mutation Checker program has been created to help researchers and database curators to verify the transription and translation effects of DNA level sequence variation.

The user is expected to give a valid reference sequence accession number, select the numbering system, and type in the start position of the change, followed by reference and variant nucleotide sequences.

The output gives details of the mutation and its effect in EMBL-like text format.

bend.it Server
This server predicts bendability and propensity to curvature from DNA sequences. This is an experimental, pre-release version.

The calculation is based on the observation that bendability is asymmetrically distributed in DNA segments that are intrinsically curved.

The server accepts DNA sequences of a maximum of 5000 nucleotides in length, given in one letter-code (A, C, G, T and white spaces are accepted). Two bendability scales are available, the one based on DNase I digestion is the default, it reflects DNA's bendability towards the major groove. A second"consensus scale" is given as an option, it is suitable for detecting intrinsically curved GC elements that are not detected by the DNase I-based scale.

The results of the calculation are bendability, curvature propensity and G+C content values listed along the sequence. The values are calculated in a sliding window (default is 30 residues). The curvature propensity is calculated with a constant twist angle value (default is 36 degrees, corresponding to ideal B-DNA).

The results are presented as:

endability or the G+C content are plotted along the DNA sequence her the bendability or the G+C content

AG BIODV - MatInd, MatInspector, ConsInd, ConsInspector, GenomeInspector, ModelInspector
Range of utilities covering:

MatInd, MatInspector

ConsInd, ConsInspector GenomeInspector ModelInspector

Translation Utility
A simple utility to translate a nucleic acid sequence into a protein.

Mutability - check sequences for potential Nonsense/Missense/Neutral mutations
Mutability will check a DNA sequence to determine how many single point mutations would result in:

It will also:

EnzFinder - A restriction engine search engine.
A restriction engine search engine. Looks on Rebase for known RE matching your query.

Find all you need to know about a RE!

MELTING: enthalpie, entropy and melting temperature
This program computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program first computes the hybridisation enthalpy and entropy from the elementary parameters of each Crick's pair by the nearest-neighbor method. Then the melting temperature is computed.

A280/A260 calculator
This can be used to calculate the molecular weight, the extinction coefficient, the concentration, and the melting temperature of a single stranded nucleic acid.

LabOnWeb is a collection of online lab protocols and life science research tools.

InstantRACE returns a full gene sequence from an EST, RNA, or mRNA sequence. InstantRACE also provides a comprehensive gene function report, based on a multistage, multiple database search.

Any Comments, Questions? Support@hgmp.mrc.ac.uk