Change Log

New features & bug fixes.

April 2021

Added

We added the Promoter Calculator in both predict and design modes. Version 1 [sigma70 only].
We added "CDS Maker Mode" for the Non-Repetitive Parts Calculator. Designs large toolboxes of highly non-repetitive protein coding sequences (same amino acid sequences). Additional constraints can be specified.
We added a site-wide Leaderboard that list the number of researchers and submitted design jobs at each academic & research institution. Commercial entities are not shown.

Fixed

We fixed an issue with memory management that could cause the browser to crash, particularly if your results contained several batch prediction or design jobs.
We removed the Alipay payment option.

February 2021

Fixed

We found that NCBI's Genome database contains genomes with missing annotations for ribosomal RNAs, including several commonly used workhorse organisms (e.g. Escherichia BL21!). Our Genome-wide Calculator pipeline uses these annotations to determine anti-Shine Dalgarno sequences (16S rRNA 3' ends) as well as synonymous codon usage tables. To fix this issue, we developed a way to impute the missing annotations. We also corrected several truncated annotations. You can view the results from our Genome-wide Calculator at https://www.denovodna.com/software/listBacteria and add new non-model bacteria to the database at https://www.denovodna.com/software/addBacteria.

January 2021

Added

Several algorithms use organism-specific calculations to predict gene expression levels and design genetic systems. You can now view those organism-specific calculations at https://www.denovodna.com/software/listBacteria. If your organism of interest is missing from an algorithm's organism selection list, you can now add it at https://www.denovodna.com/software/addBacteria. You can search using its species name, taxonomy, or NCBI accession number from an overall list of over 19000 sequenced bacterial genomes. Select one and then click submit. The organism will be then available for usage once those calculations have been completed.
We've upgraded our payment interface to utilize Stripe's new customer portal and session checkout service. Stripe is a global, secure, first-class payment processor. Payments can be made either on-line and off-line and in selected currencies (USD, euros, and yuan for now).

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April 2021

Added

We added the Promoter Calculator in both predict and design modes. Version 1 [sigma70 only].

We added "CDS Maker Mode" for the Non-Repetitive Parts Calculator. Designs large toolboxes of highly non-repetitive protein coding sequences (same amino acid sequences). Additional constraints can be specified.

We added a site-wide Leaderboard that list the number of researchers and submitted design jobs at each academic & research institution. Commercial entities are not shown.

Fixed

We fixed an issue with memory management that could cause the browser to crash, particularly if your results contained several batch prediction or design jobs.

We removed the Alipay payment option.

February 2021

Fixed

We found that NCBI's Genome database contains genomes with missing annotations for ribosomal RNAs, including several commonly used workhorse organisms (e.g. Escherichia BL21!). Our Genome-wide Calculator pipeline uses these annotations to determine anti-Shine Dalgarno sequences (16S rRNA 3' ends) as well as synonymous codon usage tables. To fix this issue, we developed a way to impute the missing annotations. We also corrected several truncated annotations. You can view the results from our Genome-wide Calculator at https://www.denovodna.com/software/listBacteria and add new non-model bacteria to the database at https://www.denovodna.com/software/addBacteria.

January 2021

Added

Several algorithms use organism-specific calculations to predict gene expression levels and design genetic systems. You can now view those organism-specific calculations at https://www.denovodna.com/software/listBacteria. If your organism of interest is missing from an algorithm's organism selection list, you can now add it at https://www.denovodna.com/software/addBacteria. You can search using its species name, taxonomy, or NCBI accession number from an overall list of over 19000 sequenced bacterial genomes. Select one and then click submit. The organism will be then available for usage once those calculations have been completed.

We've upgraded our payment interface to utilize Stripe's new customer portal and session checkout service. Stripe is a global, secure, first-class payment processor. Payments can be made either on-line and off-line and in selected currencies (USD, euros, and yuan for now).