ArticleBMC bioinformatics2006
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.BMC genomics · 2018Article
- Disruption of Visc-2, a Brain-Expressed Conserved Long Noncoding RNA, Does Not Elicit an Overt Anatomical or Behavioral Phenotype.Cerebral cortex (New York, N.Y. : 1991) · 2015Article
- IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.Evolutionary bioinformatics online · 2015Review
- SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation.BMC bioinformatics · 2011Article
- Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes.Genome biology · 2010Article
- CSA: an efficient algorithm to improve circular DNA multiple alignment.BMC bioinformatics · 2009Article
- Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences.BMC bioinformatics · 2007Article
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10 authors.
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Abstract
backgroundDeluged 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.
resultsIn 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.
conclusionWith 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.
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