TR-IIS-05-005    Fulltext

SinicView: A Visualization Environment for Comparisons of Multiple Sequence Alignment Tools

Arthur Chun-Chieh Shih, D.T. Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Chun-Yi Wong, Meng-Yuan Chou, and Tze-Chang Shiao


Deluged by completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus become available. In the initial stage of sequence analysis, a biologist usually faces with the questions about how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question about whether unaligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. Although several systematic evaluations of multiple sequence alignment programs have been proposed, they may not provide a standard-bearer for most biologists because those unaligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools could help a biologist evaluate their correctness and accuracy.


In this paper, we present a versatile alignment visualization system, called SinicView, (for Sequence-aligning INnovative and Interactive Comparison VIEWer), which allows the user to efficiently compare and evaluate assorted alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a sliding window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. The user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides along with the annotations information. With SinicView, users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment and sequence analysis. We illustrate the capabilities of our visualization system by comparing alignment results obtained by ClustalW, MLAGAN, MAVID, and MULTIZ, respectively.


keywords: Comparative genomics, multiple sequence alignment, sequence alignment visualization, web-based collaborative environment