Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Evaluating system utility and conceptual fit using CASSM

There is a wealth of user-centred evaluation methods (UEMs) to support the analyst in assessing interactive systems. Many of these support detailed aspects of use – for example: Is the feedback helpful? Are labels appropriate? Is the task structure optimal? Few UEMs encourage the analyst to step back and consider how well a system supports users’ conceptual understandings and system utility. In this paper, we present CASSM, a method which focuses on the quality of ‘fit’ between users and an interactive system. We describe the methodology of conducting a CASSM analysis and illustrate the approach with three contrasting worked examples (a robotic arm, a digital library system and a drawing tool) that demonstrate different depths of analysis. We show how CASSM can help identify re-design possibilities to improve system utility. CASSM complements established evaluation methods by focusing on conceptual structures rather than procedures. Prototype tool support for completing a CASSM analysis is provided by Cassata, an open source development