During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignmen...
Background: Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering al...
Yonghui Chen, Kevin D. Reilly, Alan P. Sprague, Zh...
For as long as biologists have been computing alignments of sequences, the question of what values to use for scoring substitutions and gaps has persisted. While some choices for s...
Background: Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations ...
Motivation: Mapping of remote evolutionary links is a classic computational problem of much interest. Relating protein families allows for functional and structural inference on u...