Computational Molecular Biology - Analytical Genomics
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Comparative in silico meta - Genomics: Annotation analyses, comparative gene regulators and gene evolution analyses,
motive conservation pattern, codon usage
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Genome Mining - identification of new genes, regulators and metabolic pathways
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Functional Genomics - Data Mining - functional analyses, predictions
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• Metabolomics and metabolic reconstructions
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• Transcriptomics and conceptual expression optimization, RNAseq analyses
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• Analytical and synthetic proteomics and structural molecular biology
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Synthetic Molecular Biology - Gene Function Oriented Computation
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Gene sequence analyses of expression relevant functional sequence parameters on different
molecular levels (DNA, RNA, Protein, Interaction level)
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In silico simultaneous multi-parameter calculations for expression optimization on different molecular levels
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• Transcriptional and translational initiation optimization
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• Translational elongation optimization
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• mRNA stability, internal secondary structures, motives (e.g.internal SD, splicingsites etc.)
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Identification and selection of regulatory genetic elements based on genomic analyses and data mining
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Assessment of functional optimization strategies for proteins e.g. enzymes
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Constructional DNA - Design Projects
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Constructional design and realization of functional gene clusters (artificial biochemical pathways, hetero-protein complexes)
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Sequence calculations for different types of gene cluster assembly strategies
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Sequence calculations for functional substitution of sequence building blocks
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• Promoter Libraries
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• Leader Libraries (TIR)
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• CDS - libraries
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We at ATG:biosynthetics over time and with support of governmental funding money developed and improved our in house knowledge and proprietary computer
programs like EvoMAG and myBioDesign along with the requirements of our customers. We are supporting our customers not only with genomic
annotations, data mining, information generation, condensation and handling. In addition we are computing optimal sequence compositions for constructive
and functional gene and gene cluster designs. In silico gene evolution with multi-target parametric are Pareto optimized. Please inquire for any problem
you have in constructive and designing multi-gene applications in gene clusters for metabolic pathways (anabolic and catabolic), hetero-protein complexes
and multiple constructive elements like for metabolic channeling etc.
Examples processed by ATG
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| Bioproduction Product |
Pathway in kb |
Application |
Constructional Design |
Expression Optimization |
Leader-Library |
Specific Vector: Design & Syntheses |
| Epothilone |
65 |
Cytostatic |
yes |
yes |
yes/no |
yes |
| ω-3-PUFA |
31,4 |
Essent. Fatty Acid |
yes |
yes |
yes |
yes |
| Argyrin |
37,2 |
Antibiotic |
yes |
yes |
yes |
yes |
| MethylMalonylCoA |
18,8 |
Metabolic |
yes |
yes |
no |
yes |
| MyxoChromid |
32 |
Antibiotic |
yes |
yes |
no |
yes |
| Coronatin |
36 |
Phytotoxin |
yes |
no |
no |
yes |
| Bottromyicin |
20 |
Antibiotic |
yes |
no |
no |
yes |
| Myxopyronin |
53,4 |
Antibiotic |
yes |
no |
no |
yes |
| Glumicin |
35,2 |
Antibiotic |
yes |
no |
no |
yes |
| Magnetit |
8,9 |
Geotropism |
yes |
no |
no |
yes |
| 5-Hetero-Proteins Complex |
10,4 |
Regulation on Protein Level |
yes |
no |
no |
yes |
| Multiple Glycosyl-transferase Genes |
9,5 |
Glycosyl-ation |
yes |
no |
no |
yes |
Decoupling of DNA - syntheses from constructional and functional gene design was anticipated as early as SB2.0 in Berkeley 2006.
This process, which is in a direct analogy to the manufacturing of hard discs and memory sticks now seems to approach its finalization.
On the other side of the coin is the very interesting topic of predictive functional programming of genes for desired application purposes.
It accumulated high levels of knowledge over the time frame of the last years not only in the scene of protagonists like Mutalik VK et al. (2013),
Goler et al. (2008) and Andrianantoandro E. (2006) but Rössger K et al. (2013) and Arkin AP and Fussenegger M. (2013) even on very high impact.
But also in company environments with academic and company clients many projects are realized straight along to the customers desires and ideas without
the high visibility on the list of authors of publications.
Arkin AP, Fussenegger M. (2013) Curr Opin Chem Biol. Dec;17(6):869-70. doi:
10.1016/j.cbpa.2013.11.005. Epub 2013 Nov 20. Synthetic biology.
Rössger K et al. (2013) A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun. Nov 26;4:2825. doi:
10.1038/ncomms3825.
Mutalik VK et al. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods, doi:10.1038/nmeth.2404.
Andrianantoandro E et al. (2006) Synthetic biology: new engineering rules for an emerging discipline Molecular Systems Biology doi:10.1038/msb4100073.
Goler et al. (2008) Genetic design: rising above the Sequence, Trends Biotechnol., 26:538-44
