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Expression Online Tutorial Overview

Genamics Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Below is an overview of the features of Genamics Expression. More information about each feature is provided, mostly in the form of easy-reading tutorials, on how to analyse your sequences and get the most out of Expression. Background information and references are also provided to explain how the actual processes are calculated.

Core Interface

Annotating Your Sequences
Expression offers powerful and flexible features to allow you to directly annotate your sequences. This revolutionary system eliminates the cumbersome position counting to locate notable sequence patterns, structures, or motifs. The sequence annotations are rendered real-time on the graphical sequence map (see below), so the complexity of a sequence may be traversed with ease. Discover the world of possibilities sequence annotation brings to sequence analysis.

Using the Sequence Map
Graphical sequence maps are created real-time from the amino acid or DNA sequence in the editor. The unique annotation ability of the editor makes it possible to effortlessly create publishable quality graphical representations of your sequences. The Sequence Map is also fully interactive, which makes navigating around large sequences a breeze.

Internet Tools

Importing Sequences from GenBank and Other Sources
GenBank can be browsed and queried from directly within Expression, then imported with a single click directly for further analysis. Sequences from GenBank are automatically annotated using the information associated with GenBank entry. Coupled with the Graphical Sequence Map (see above), an interactive visual representation of any sequence stored in GenBank can be displayed effortlessly

Using ProScan to Identify Protein Signatures
ProScan utilises the PROSITE database of protein sites and signatures, to identify biologically relevant regions.

Aligning Multiple Sequences and Generating a Consensus
DNA or amino acid sequences can be aligned with ease, using either the MultAlin or ClustalW algorithms. Consensus sequences from the alignment are automatically generated and can be further analysed by Expression.

Predicting the Secondary Structure of Your Protein
The secondary structure of amino acid sequences can be predicted using any of variety of algorithms, including GOR IV, HNN, Predator, and SOPMA.

Windows Tools

Restriction Mapping and Analysis
DNA sequences can be analysed almost instantaneously with the powerful Digester tool. Publication-quality restriction maps of linear or circular DNA are created on the fly. Appropriate enzymes can be rapidly identified by screening based on name or a variety of properties, including recognition site, fragment pattern, and cut frequency.

Identifying Open Reading Frames
Likely open reading frames (ORFs) in DNA sequences can be easily found using the ORF Mapper tool. By adjusting the threshold coding length, identification of bonafide genes is simple.

Finding Patterns and Motifs in DNA or Protein Sequences
The Patter Finder tool makes it easy to find exact or near match amino acid or DNA sequences in a target sequence. DNA sequences can be translated in all possible reading frames on the fly, to allow identification of a particular amino acid sequence.

Reverse Translation and Handling Ambiguous Characters
Amino acid sequences can be reverse translated into degenerate (ambiguous) DNA code. Expression has extensive support for both ambiguous DNA and degenerate amino acid characters.

Designing Primers for PCR
Primer pairs are computed from the set target regions, then screened against a series of parameters to maximise priming efficiency. The powerful real-time interface allows the rapid identification of the theoretical ideal primers for the region to be PCR amplified.

DNA and Protein Properties Calculator
All the typical sequence properties are provided by the Calculator Tool, including molecular weight determination, GC content and absorbance factor calculation, amino acid content etc.

Genamics Expression Online Tutorial Overview

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