There has been accumulating evidence in recent years that certain F0 events are consistently aligned with segmental events such as the syllable boundary. The mechanisms for the observed alignment patterns, however, are still being closely investigated. In this paper I argue that to understand the observed tonal alignment patterns, it is imperative to first understand the role of articulatory co...

Given two sequences S1, S2 and a constrained sequence C, the longest common subsequence of S1, S2 with restriction to C is defined as the constrained longest common subsequence (CLCS) of S1, S2 and C. At the same time, the best alignment of S1, S2 with restriction to C is defined as the constrained pairwise sequence alignment (CPSA) of S1, S2 and C. Previous algorithms have shown that both CLCS...

When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts to find useful alignment constraints that can reduce the co...

This paper examines the usefulness of constraintbased alignment and distribution tools in graphical editors. Currently one-way constraints are used to provide alignment and distribution tools in many commercial editors. In this paper we discuss how limitations of oneway constraints lead to serious usability issues with such tools. To overcome these limitations, we show how to implement alignmen...

The secondary stress pattern of Spanish occupies a key position in current debates in metrical stress theory. It is one of the patterns potentially capable of discriminating between accounts where distance-sensitive alignment constraints play a central role (McCarthy and Prince 1993, Gordon 2002, Hyde 2002) and accounts where they play a more restricted role (Alber 2005) or no role at all (Kage...

MOTIVATION A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a co...