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Welcome to the GenomeWeb Nucleic Acid General Sequence Analysis Analysis Search for:

NCSA BIOLOGY WORKBENCH
BCM Search Launcher
Cutter - restriction mapping tool
DNA Mutation Checker
bend.it Server
AG BIODV - MatInd, MatInspector, ConsInd, ConsInspector, GenomeInspector, ModelInspector
RepeatMasker - mask out repeat sequences
CENSOR - mask out repeat sequences
TACG - Restriction Enzyme Mapping and Analysis
Translation Utility
Mutability - check sequences for potential Nonsense/Missense/Neutral mutations
A280/A260 calculator

Detailed information on the above options

NCSA BIOLOGY WORKBENCH
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

• Protein sequence/pattern searches (with highlighting of protein domains found)
• Nucleic acid sequence searches
• Multiple sequence alignments
• Pairwise sequence alignments
• Gene feature searches
• Sequence utilities
• Protein secondary structure prediction

• BCM Gene Finder
• BCM protein secondary structure prediction
• The Biologist's Control Panel
• YAC data searches

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

• Customizable enzyme database
• Monthly enzyme updates
• Automatic sequence search-and-input
• Quick links to gene searches

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:

• An ASCII file
• An optional sequence-plot, in which the curvature propensity and either the b

• An optional 2D plot, in which the curvature propensity is plotted against eit

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

MatInd, MatInspector

• Fast consensus definition and recognition based on a matrix approach.
• This software including a large library of protein binding site matrices (>200) is available from this site!!!

• Advanced consensus definition and recognition.
• ConsInspector together with a library of protein binding site descriptions is available here.

• Fast large scale correlation analysis of genetic structures.
• Especially for the use on large sequences like chromosomes as they are being gathered by the Yeast Sequencing Project or the Human Genome Project.

• Recognition software for determination and detection of complex genetic structures, for example LTRs

RepeatMasker - mask out repeat sequences
RepeatMasker screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.

CENSOR - mask out repeat sequences
The CENSOR web server allows users to have query sequences aligned against a reference collection of human or rodent repeats (Jurka, et al., 1992; Jurka, 1995b). The homologous portions are then "censored". Censoring means replacing the aligned portions with x's in the query sequences. The server automatically classifies all known repeats and adds the classification to the report.

The query sequence(s) must be in Stanford/IG format. A Stanford/IG sequence begins with one, or more, sequence description or comment lines which begin with a semi-colon, ";". Following the comments is a single line with the sequence's locus name (up to 12 characters). And following are one or more lines of sequence data, these may be lower- or upper-case.

TACG - Restriction Enzyme Mapping and Analysis
TACG is a character-based, command line tool for the restriction enzyme analysis of DNA for unix-like operating systems.

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:

• Nonsense mutations
• Missense mutations
• Neutral mutations

• Print the sequence with potential STOP codons highlighted
• Count the number of CpG sites in the sequence
• Print the sequence with CpG sites highlighted

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.