There are three viewing sections in SinicView: Global View, Detailed View, and Information View (including annotations and gaps.) The Global View section shows the whole percent identity plots that calculate the sum-of-pair scores based on one specified reference sequence. In the Detailed View section, the panels show the whole percent identity plots of different alignment results individually. By observing the graphical results, it is much more intuitive and straightforward to judge the consistency of the alignment results. When the sliding window is less than 100 base pairs, the Detailed View section will automatically switch from the curve-based plot to the display of the detailed alignments in a colored text format where identical characters are shown. The Information View section containing annotation and gap information is stacked beneath the Detailed View section. SinicView also provides several global comparison charts that can assist biologists to choose the best alignment result among those produced by the programs under consideration. SinicView is implemented entirely in Java language to ensure portability across major platforms and is accessible with a web browser and Internet connection. The main features of SinicView are summarized as follows:
1. Visualization of the scoring distribution of alignment results in a curve-based graphic format;
2. Generation of the comparison charts using stacked-bar and pie charts, which shows the distribution of the identical rates among various alignment programs for benchmarking purposes;
3. Inclusion of a versatile manipulative functionality (gap-display toggling, drag-and-drop zooming/shifting, and graphic/text display toggling);
4. Visualization of annotation information and display of the phylogenetic trees provided by users in which the drawing tree program uses the ATVtree [49
5. Visualization of detailed text alignments results;
6. Capability to export the visualization results to portable image files.
In what follows, we will introduce the characteristics and functionality of SinicView in more detail.
Manipulative operations in SinicView
SinicView offers a series of manipulative and navigational controls, such as zooming, shifting, and gap/annotation toggling. As shown in Figure , SinicView displays the alignment results obtained by three different MSA methods. The input sequences contain the orthologous regions around the Stem Cell Leukemia (SCL) gene in five vertebrate species: human, mouse, chicken, pufferfish and zebrafish. The buttons and text-field boxes of manipulative functions are located on top of the frame. Users can manually input numerical values or click on the highlighted colored region in the Global View section that specifies the zooming or shifting factors in a drag-and-drop fashion. When the highlighted region is clicked and dragged, the equivalent of a shift action will be performed and the display region can be resized by adjusting the edge of the highlighted area.
The screenshot shows the user interface of SinicView. The alignment result is of the SCL gene regions in human, mouse, chicken, pufferfish, and zebrafish. Three alignment results of five sequences aligned by ClustalW, MAVID, and MLAGAN are shown.
SinicView can display more than one alignment result obtained by different alignment programs (either pairwise or multiple ones.) The assorted mixed-color span under the Global View panel shows among the alignment tools used the preferred aligner, which generates comparatively better results on the spot. Each of the aligners is denoted by a pre-defined color with the "performance color" label right next to the name of the tool.
Multi-panel functionality in SinicView
In the Detailed View section, the Percent Identity Plot (PIP) panels show, from top to bottom, the similarity curves of the alignment results obtained by different programs, along with the names of the alignment tools. In the Information View section, the Gap & Annotation panels (in pink and gray) display the information of annotations provided by users, and gaps of aligned sequences. The information and similarity ratios can also be displayed as the current scan-line (i.e. cursor) moves. The boxes in maroon denote the annotation area and the horizontal line represents the original sequences interleaved with inserted gaps (light gray areas.) The gap display can be toggled on or off via the checkbox on the right.
Because different alignment results are usually of different lengths, it is not plausible to compare these results base-pair by base-pair. In SinicView, therefore, we let users select one of input sequences as a reference and then calculate the sum-of-pair scores of each base pair in the reference within a fixed window. For example, each alignment result in the PIP panels at the scan-line position corresponds to human sequence, selected as the reference in Figure . When the user selects different sequences as the reference, SinicView can demonstrate the variations between the PIP curves of the alignment results.
Visualization of SinicView: comparison chart and text-mode comparison
The functionality under the "Tools" menu, called "Comparison Charts", offers two types of charts for quick-and-easy evaluation of the alignment quality. The stacked bar chart, in Figure , illustrates the distribution of the identical rates with the threshold over 40%. The pie chart, on the other hand, displays the distribution of the identical rates from 0 to 100 percent based upon a selected alignment program. The statistics on which these charts are based can also be displayed in a tabulated text form.
Figure 2 The tools menu functions. Two comparison charts can be generated by SinicView: the stacked-bar chart illustrates the proportion comparison of cross alignment results and the pie chart shows the proportion of different identical rates of an individual (more ...)
SinicView also provides a plain-text view of the alignment results in the Detailed View section when the sliding window size is less than 100 aligned base pairs. As shown in Figure , the plain-text alignment results replace the percent identity curves and the fully identical bases in a column are labeled in red blocks. Thus, users can check the correctness of detailed alignment results base pair by base pair.
The detailed text display of the different alignment results. The matched identical sequences are labeled in red blocks. Interestingly, all three results do not contain consistent matching alignments in this case.
Installation and execution of the standalone SinicView
The applet version can be accessed via any JRE (Java Runtime Environment)-enabled browsers with Internet connection, thus making the installation and choosing the right platform hassle-free. However, the ease of running SinicView on-the-go cannot accommodate the bandwidth requirement in case of huge amount of sequence data involved. Hence, we have also implemented a standalone application of SinicView, which is wrapped in JRE, for off-line use.
The execution procedure of the standalone SinicView is quite straightforward. Upon launch, the user will be prompted three options. The first two are to read user's Phylogenetic Tree files, an option, and MSA results from the local disk.