Finite-temperature local protein sequence alignment: percolation and free-energy distribution

Understand

Sequence alignment is a tool in bioinformatics that is used to find homological relationships in large molecular databases.

• It can be mapped on the physical model of directed polymers in random media.
• We consider the finite-temperature version of local sequence alignment for proteins and study the transition between the linear phase and the biologically relevant logarithmic phase, where the free-energy grows linearly or logarithmically with the sequence length.
• By means of numerical simulations and finite-size scaling analysis we determine the phase diagram in the plane that is spanned by the gap costs and the temperature.