SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools

Arthur Chun Chieh Shih, D. T. Lee, Laurent Lin, Chin Lin Peng, Shiang Heng Chen, Yu Wei Wu, Chun Yi Wong, Meng Yuan Chou, Tze Chang Shiao, Mu Fen Hsieh

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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. Conclusion: 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.

Original languageEnglish
Article number103
JournalBMC Bioinformatics
Volume7
DOIs
Publication statusPublished - Mar 2 2006
Externally publishedYes

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Sequence Alignment
Nucleotides
Sequence Analysis
Alignment
Visualization
Research Design
Scoring
Genomics
Multiple Sequence Alignment
Evaluate
Evaluation
Annotation
Correctness
Choose
Calculate

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

SinicView : A visualization environment for comparisons of multiple nucleotide sequence alignment tools. / Shih, Arthur Chun Chieh; Lee, D. T.; Lin, Laurent; Peng, Chin Lin; Chen, Shiang Heng; Wu, Yu Wei; Wong, Chun Yi; Chou, Meng Yuan; Shiao, Tze Chang; Hsieh, Mu Fen.

In: BMC Bioinformatics, Vol. 7, 103, 02.03.2006.

Research output: Contribution to journalArticle

Shih, ACC, Lee, DT, Lin, L, Peng, CL, Chen, SH, Wu, YW, Wong, CY, Chou, MY, Shiao, TC & Hsieh, MF 2006, 'SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools', BMC Bioinformatics, vol. 7, 103. https://doi.org/10.1186/1471-2105-7-103
Shih, Arthur Chun Chieh ; Lee, D. T. ; Lin, Laurent ; Peng, Chin Lin ; Chen, Shiang Heng ; Wu, Yu Wei ; Wong, Chun Yi ; Chou, Meng Yuan ; Shiao, Tze Chang ; Hsieh, Mu Fen. / SinicView : A visualization environment for comparisons of multiple nucleotide sequence alignment tools. In: BMC Bioinformatics. 2006 ; Vol. 7.
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