Paper Info
Title
SinicView: an interactive visualization tool for comparison of multiple sequence alignment results
Abstract
In the initial stage of sequence analysis, a biologist is first faced 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. In this paper, we present a versatile alignment visualization system, called SinicView, (for sequence-aligning innovative and interactive comparison viewer), which allows users 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. Combined with the annotations information, the user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides. 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. SinicView is avaiable for free download from http://biocomp.iis.sinica.edu/.
Year
DOI
Venue
2005
10.1109/CSBW.2005.127
CSB Workshops
Keywords
Field
DocType
sliding window,nucleotide,cellular biophysics,sinicview,interactive comparison viewer,genetics,graphic scoring profile,scoring system,visualization system,multiple sequence alignment results,multiple sequence alignment,versatile alignment visualization system,sum-of-pairs method,interactive visualization tool,alignment output,assorted alignment result,annotations information,biology computing,molecular biophysics,visualization tool,data visualisation,sequence-aligning innovative,inappropriate alignment tool,alignment result,sequence analysis,graph theory,best tool,various alignment tool,nucleotides,sequence alignment,interactive visualization,visual system
Graph theory,Data visualization,Sliding window protocol,Computer science,Visualization,Plain text,Interactive visualization,Bioinformatics,Multiple sequence alignment,Sequence analysis
Conference
ISBN
Citations 
PageRank 
0-7695-2442-7
0
0.34
References 
Authors
0
8
Name
Order
Citations
PageRank
Arthur Chun-Chieh Shih11028.29
D. T. Lee224181083.30
Laurent Lin3261.31
Chin-Lin Peng4753.93
Shiang-Heng Chen5250.92
Chun-Yi Wong6250.92
Meng-Yuan Chou7493.73
Tze-Chang Shiao8250.92