title: An investigation of conservation-biased gap-penalties for multiple protein sequence alignment.
abstract: Sequence conservation in a multiple sequence alignment (or profile) is often used to influence the alignment of further sequences onto the profile. Most methods, however, have considered only the opening of a gap at a single point and not what is contained in the inserted segment of one sequence (or profile) or what terminates the 'broken' ends of the other. An alignment algorithm is described that incorporates these aspects and the relative importance of the contribution from the insert and the 'broken' ends has been assessed. The approach was tested on families of very remotely related sequences using a novel protocol that was developed to quantify both the stability and generality of the solution.
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D017124:Conserved Sequence; D008962:Models, Theoretical; D016415:Sequence Alignment; D017421:Sequence Analysis