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 language | English |
|---|---|
| Article number | 103 |
| Journal | BMC Bioinformatics |
| Volume | 7 |
| DOIs | |
| Publication status | Published - Mar 2 2006 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - SinicView
T2 - A visualization environment for comparisons of multiple nucleotide sequence alignment tools
AU - Shih, Arthur Chun Chieh
AU - Lee, D. T.
AU - Lin, Laurent
AU - Peng, Chin Lin
AU - Chen, Shiang Heng
AU - Wu, Yu Wei
AU - Wong, Chun Yi
AU - Chou, Meng Yuan
AU - Shiao, Tze Chang
AU - Hsieh, Mu Fen
PY - 2006/3/2
Y1 - 2006/3/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33645669722&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33645669722&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-7-103
DO - 10.1186/1471-2105-7-103
M3 - Article
C2 - 16509994
AN - SCOPUS:33645669722
VL - 7
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
M1 - 103
ER -