It is widely accepted that the optimal alignment between a pair of proteins or nucleic acid sequences that minimizes the edit distance may not necessarily re
ect the correct biolog...
Background: Proteins that evolve from a common ancestor can change functionality over time, and it is important to be able identify residues that cause this change. In this paper ...
Background: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-ba...
Frederick A. Matsen III, Robin B. Kodner, E. Virgi...
Background: We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentap...
Giovanni Capone, Giuseppe Novello, Candida Fasano,...
Background: At intermediate stages of genome assembly projects, when a number of contigs have been generated and their validity needs to be verified, it is desirable to align thes...