Using gene expression? Do you still use run-of-the-mill codon usages retrieved from public databases? You may jeopardize the success of your expression projects. Ready-made codon usages such as those from the Kazusa database are created by averaging over a set of all known open reading frames for an organism. By using such a codon usage, you are missing out on an important optimization potential.

Codon Census – a codon usage tailored towards your needs

This new service by Entelechon provides custom-made codon usage tables which are specifically developed for your purposes – taking into account your expression host, the intended expression level, localization of the expression product and many other features relevant to you. It draws data from a wide range of sources, including – where available – sequencing and expression profile data provided by you.

Codon census is based on:

• Hand-picked high expressing genes from your target organism
• A reference list of carefully curated housekeeping genes, with a particular focus on ribosomal genes
• A solid set of evaluation metrics for the codon usage bias of your expression host
• A detailed analysis of the known open-reading frames of your target organism, including clustering and the analysis of multiple codon usage preferences within the same organism.
• Position-specific codon usage preferences: Comparing codons at the 5′ and 3′ end of a gene
• Expression data from quantitative transcriptomics and proteomics studies (where available)
• Sequencing data provided by you, such as ESTs – we can analyze ESTs to detect open reading frames

The ultimate codon usage table

Using the strategies outlined above leads to codon usage tables which are much better suited for high expression optimization than standard averaged tables. If you want to go beyond publicly available data, we can do wet lab work to determine the ultimate codon usage table:

We can design and conduct a microarray experiment to determine the transcription levels of potential reference proteins, and we can perform quantitative proteomics on select target proteins to obtain very accurate absolute quantities of natural host proteins. Using these data we can then compile a very specific, accurate codon usage table for your expression setting.

Stay up-to-date

Codon census can track new sequences, transcriptomics and expression data discovered for your target organism. You can subscribe to a continuous survey of the public databases, with an automated monthly report on new findings. This will ensure that your tailor-made codon usage table reflects the best current knowledge about your target organism.

More information

To get more information about Codon Census, please use our inquiry and order page or go directly to our customer database to send an inquiry. We will be happy to discuss your specific requirements and provide you with a detailed price quote.

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