SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools.
BACKGROUND
Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of 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 of whether poorly aligned 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 (MSA) programs have been proposed, they may not provide a standard-bearer for most biologists because those poorly aligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy.


RESULTS
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 nucleotide alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a fixed 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. We illustrate the capabilities of our visualization system by comparing alignment results obtained by MLAGAN, MAVID, and MULTIZ, respectively.


CONCLUSIONS
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 in the initial stage of sequence analysis.
Shih
Arthur Chun-Chieh
AC
Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. arthur@iis.sinica.edu.tw
Lee
D T
DT
Lin
Laurent
L
Peng
Chin-Lin
CL
Chen
Shiang-Heng
SH
Wu
Yu-Wei
YW
Wong
Chun-Yi
CY
Chou
Meng-Yuan
MY
Shiao
Tze-Chang
TC
Hsieh
Mu-Fen
MF
D000465:Algorithms; D001483:Base Sequence; D003196:Computer Graphics; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface