Genome Analysis
Decoding the blueprint of life by integrating physicochemical principles with cutting-edge computational methods.
Beyond the Sequence
DNA is more than a sequence of A, T, G, and C. It is the blueprint of life, encoding not just protein-coding genes but also non-coding RNAs and regulatory elements such as promoters, enhancers, and exon–intron boundaries that shape how genes are expressed.
This complexity makes genome annotation—the identification of functional elements in newly sequenced genomes—one of the most challenging problems in molecular biology. Accurate annotation is essential for mapping genome organization, understanding cellular processes, and uncovering the genetic basis of disease.
The Ab-initio Approach at SCFBio
Traditional annotation methods rely on consensus motifs or comparisons to reference genomes. While powerful, they often fall short for non-model organisms or where sequence signals are weak. Ab-initio analysis offers another path, leveraging the intrinsic physicochemical and structural properties of DNA itself.
At SCFBio, we have pioneered this approach. Our work extends beyond simple sequence analysis, focusing on the biophysical descriptors of DNA derived from extensive molecular dynamics simulations. This principle—that sequence dictates structure, and structure dictates function—applies as much to nucleic acids as it does to proteins.
Early Models: Gene Evaluator & Predictor
Our initial work used a three-parameter model (hydrogen bonding, stacking energy, interaction potentials) to robustly characterize gene vs. non-gene regions in prokaryotes across all six reading frames.
Advanced Tools: SEProm & ChemEXIN
Building on this foundation, we developed SEProm for prokaryotic promoter prediction and ChemEXIN, a deep-learning framework for detecting exon–intron boundaries in eukaryotes.
The Future: The Genome Reader
Our next step is the Genome Reader, a platform now under development. It will consolidate our findings into a practical system for genome annotation, scalable across species and grounded in the universal language of DNA’s structural and energetic properties.