Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUS...
The alignment of multiple protein (or DNA) sequences is a current problem in Bioinformatics. ClustalW is the most popular heuristic algorithm for multiple sequence alignment. Pairw...
Carlos R. Erig Lima, Heitor S. Lopes, Maiko R. Mor...
The common-use gap penalty strategies, constant penalty and affine gap penalty, have been adopted in the traditional three-sequence alignment algorithm which considers the inserti...
Abstract-In this paper, we improve the idea of the near-optimal alignments. Though the near optimal alignments increase the possibility to find the correct alignment, too many of t...
Background: Profile-based analysis of multiple sequence alignments (MSA) allows for accurate comparison of protein families. Here, we address the problems of detecting statistical...