Background: Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. Howeve...
Paolo Ferragina, Raffaele Giancarlo, Valentina Gre...
Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequence...
Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, J...
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...
Abstract: We present a method for simultaneous three-dimensional (3D) structure generation and pharmacophorebased alignment using a self-organizing algorithm called Stochastic Prox...
This paper compares different bilexical tree-based models for bilingual alignment. EM training for the new model benefits from the dynamic programming "hook trick". The ...