To study the protein folding problem, we use exhaustive computer enumeration to explore “sequence space soup,” an imaginary solution containing the “native” conformations (i.e., of lowest free energy) under folding conditions, of every possible copolymer sequence. The model is of short self-avoiding chains of hydrophobic (H) and polar (P) monomers configured on the two-dimensional square lattic...

The ability to extract and characterize genomic DNA fragments from mixed microbial assemblages is providing novel insights into the ecology, evolution, and metabolism of uncultured microorganisms in nature.

Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as "unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as "biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researche...