Basic Sequence Analysis and Annotation Laboratory

Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats. Availability:Combo is integrated as part of the ArgoGenomeBrowser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs onmultiple platforms and is freely available for download at http://www.broad.mit.edu/annotation/argo/. Contact: reinhard@broad.mit.edu Whole genome comparisons provide a powerful means for identifying large scale evolutionary changes between organisms and conserved sequences, such as genes and other functional elements. A number of applications have been developed for visualizing comparative data. One effective paradigm is the dot plot. Utilities based on this paradigm include Dotter (Sonnhammer and Durbin, 1995) and gff2aplot (Abril et al., 2003). Though dot plots are an excellent way of giving a high level overview of large, complex regions, they are less suited for close detail. Furthermore, existing dot plot based utilities do not provide a dynamic user interface or a rich display of sequence annotations along with the alignment data. A second paradigm for comparative data is to link a representation of two different sequences through polygons or trapezoids. This ‘parallel’ approach is used in the GAME synteny viewer of the Apollo browser (Lewis et al., 2002), the Artemis Comparison Tool (ACT) (Carver et al., 2005) and the Ensembl MulticontigView (Hubbard et al., 2005). Though this paradigm is effective at small scales, it breaks down as regions grow large or map to multiple locations. To combine the strengths of these two paradigms, while overcoming their limitations, we have developed a tool called Combo, which provides a dynamic view of the whole genome alignment of two sequences along with their associated annotations. Combo is the only dynamic comparative genome browser that provides both perpendicular (dot plot) (Fig. 1A) and parallel views (Fig. 1B). Combo is also unique for its intuitive, consumer grade UI— including bookmarks, tabbed browsing, dynamic zooming, UI based configuration and native OS look and feel. Combo’s perpendicular view consists of four main parts: Dot Plot Panel Horizontal (Reference) Feature Map Vertical (Query) Feature Map Inspector Panel The Dot Plot Panel displays the alignment of the two genome sequences as a set of local alignment segments. Alignments can be generated by different alignment programs [e.g. PatternHunter (Ma et al., 2002; Li et al., 2004) or BLAST (Altschul et al., 1990)] and are loaded from a flat file. Each local alignment is displayed as a line in the dot plot positioned according their coordinates. The Horizontal Feature Map displays annotations for the sequence corresponding to the horizontal axis of the dot plot. Annotations are denoted by arrows colored according to the type of annotation (e.g. gene, BLAST hit, etc.). Similarly, the Vertical Feature Map displays annotations for the vertical axis sequence. The Inspector Panel displays detailed information about selected alignments or features. For example, when an alignment is selected, the inspector will display properties of the alignment including length, percent identity and score (see Fig. 1). The dot plot and the feature maps are zoomable and scrollable, allowing users to view genome alignments at resolutions ranging from whole chromosomes to individual bases. When zoomed in, users can navigate any region of the dot plot or feature maps. Combo synchronizes the dot plot and the feature maps during zooming and navigation. For example, when users zoom in or out of the dot plot, the feature maps automatically adjust their visible ranges to match. Combo provides cross-boundary highlighting for selected objects to allow users to quickly identify corresponding genomic regions among components. When an alignment is selected, Combo highlights in yellow the sequence ranges it spans in both the horizontal and vertical dimensions. The same ranges are also highlighted in the feature maps. Likewise, if a feature or a user-defined sequence segment is selected in a feature map, Combo highlights the corresponding sequence region in that feature map and the dot plot. To whom correspondence should be addressed. 1782 The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org The perpendicular view enables viewing multiple whole genome alignments to a single reference genome. The reference genome is represented by a single horizontal feature map and query genomes are represented as multiple vertical feature maps stacked side by side. The perpendicular view provides users with a global view of genome alignments while also facilitating the identification of regions of interest. The parallel view allows viewing such a region in greater detail. This view consists of three principal components: Alignment Panel Reference Feature Map Query Feature Map As with the perpendicular view, the two Feature Maps display annotations for aligned genome sequences. The Alignment Panel, positioned between the Feature Maps, displays local alignments between the two genome sequences as trapezoids. All three panels are synchronized and highlighting features in one panel highlights corresponding regions and features in the others. Combo can load sequence annotation data from the Calhoun system or text files in GFF or FASTA format. It can import alignment data from BLAST (Altschul et al., 1990) and PatternHunter (Ma et al., 2002; Li et al., 2003) output files, as well as in a simple tab-delimited format. Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities as well as visualization for pairwise genome comparison. Argo is developed in Java, runs on multiple platforms, and is freely available for download at http://www.broad.mit.edu/ annotation/argo/. Source code is available on request. ACKNOWLEDGEMENTS We gratefully acknowledge Alan Derr and Patrick Tan for testing. This work was supported by funds from the NIH. Conflict of Interest: none declared.