The alignment and mapping of large genomic sequences is the focus of much recent research. However, relatively little has been done so far about testing and validating alignment methods. We introduce criteria and new tools we have developed for alignment evaluation. These tools have already proved useful in the evaluation and ranking of several methods for assembly-to-assembly mapping, which we...

Multiple sequence alignment is a key problem to most bioinformatics applications. The last ten years have witnessed a big improvement to existing multiple alignment tools and the development of new ones. Various parallel architectures have been experimented for reaching the highest level of accuracy and speed. This paper surveys most popular tools to clarify how parallelism accelerates the proc...

Protein sequence alignment has become an essential task in modern molecular biology research. A number of alignment techniques have been documented in literature and their corresponding tools are made available as freeware and commercial software. The choice and use of these tools for sequence alignment through the complete interpretation of alignment results is often considered non-trivial by ...

Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical u...

MOTIVATION To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool that dynamically couples a multiple sequence alignment editor to a molecular graphics display. DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein ...

We describe the course of a hackathon dedicated to the development of linguistic tools for Tibetan Buddhist studies. Over a period of five days, a group of seventeen scholars, scientists, and students developed and compared algorithms for intertextual alignment and text classification, along with some basic language tools, including a stemmer and word segmenter. keywords Tibetan; hackathon; ste...

In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a single parallel paradigm. We compare these tools to their porting onto the Fa...