In this paper, we present an algorithm to simultaneously align three biological sequences with affine gap model and infer their common ancestral sequence. Our algorithm can be fu...
Abstract. This paper addresses the problem of aligning multiple sequences of non-coding RNA genes. We approach this problem with the biologically motivated paradigm that scoring of...
Background: We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a q...
Background: Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or ...
Ribonucleic acid (RNA) molecules contain the genetic information that regulates the functions of organisms. Given two different molecules, a preserved function corresponds to a pr...