Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments

Abstract

In vitro selection experiments in biochemistry allow for the discovery of novel molecules capable of speci- fic desired biochemical functions. However, this is not the only benefit we can obtain from such selection experiments. Since selection from a random library yields an unprecedented, and sometimes comprehen- sive, view of how a particular biochemical function is distributed across sequence space, selection exper- iments also provide data for creating and analyzing molecular fitness landscapes, which directly map function (phenotypes) to sequence information (genotypes). Given the importance of understanding the relationship between sequence and functional activity, reliable methods to build and analyze fitness landscapes are needed. Here, we present some statistical methods to extract this information from pools of RNA molecules. We also provide new computational tools to construct and study molecular fitness landscapes.