CGAS: comparative genomic analysis server.

SUMMARY: Comparative approach is one of the most essential methods for extracting functional and evolutionary information from genomic sequences. So far, a number of sequence comparison tools have been developed, and most are either for on-site use, requiring program installation but providing a wide variety of analyses, or for the online search of user's sequences against given databases on a server. We newly devised an Asynchronous JavaScript and XML (Ajax)-based system for comparative genomic analyses, CGAS, with highly interactive interface within a browser, requiring no software installation. The current version, CGAS version 1, provides functionality for viewing similarity relationships between user's sequences, including a multiple dot plot between sequences with their annotation information. The scrollbar-less 'draggable' interface of CGAS is implemented with Google Maps API version 2. The annotation information associated with the genomic sequences compared is synchronously displayed with the comparison view. The multiple-comparison viewer is one of the unique functionalities of this system to allow the users to compare the differences between different pairs of sequences. In this viewer, the system tells orthologous correspondences between the sequences compared interactively. This web-based tool is platform-independent and will provide biologists having no computational skills with opportunities to analyze their own data without software installation and customization of the computer system.
AVAILABILITY AND IMPLEMENTATION: CGAS is available at http://cgas.ist.hokudai.ac.jp/.

1 INTRODUCTION

A number of comparative studies of genomic data have shown that sequence comparison is invaluable for obtaining functional and evolutionary information in genomic data. Conservation patterns along genome sequences are well studied with comparative genomics tools, including MultiPipMaker (Schwartz et al., 2003) and the UCSC genome browser (Karolchik et al., 2008). However, these tools do not directly show the collinearity between the sequences compared, although it is an important information source about genome evolution, such as duplication, inversion, translocation, insertion and deletion. Collinearity is also known as an evolutionary signal of orthology (von Mering et al., 2003).

To view the collinearity between sequences, we usually use a 2D representation, called dot plot or Harr plot, or a synteny map. A number of tools to draw a dot plot have been developed (e.g. Abril et al., 2003; Schwartz et al., 2000; Sonnhammer and Durbin, 1995; Wilson et al., 2001), but except a few, e.g. Dotter (Sonnhammer and Durbin, 1995), they do not provide interactive zooming, windowing and/or scrolling functionality. These functions are very useful when we explore a huge dot plot between big sequences like eukaryote chromosomes to identify evolutionary changes. For identification of such changes, the annotation data of and other associating data with the sequences involved in the changes may be a good help. Some interactive dot plot tools show annotation data of the sequences (Engels et al., 2006; Jareborg and Durbin, 2000; Wilson et al., 2001), but they are on-site programs, i.e. the users should install them on the platforms that the developers specify.

Here, we newly developed a comparative genomic analysis server, CGAS for viewing similarity relationships between user's sequences with their annotation information. The Asynchronous JavaScript and XML or Ajax technology is integrated into this system to provide a dynamic and user-intuitive interface, which allows the users to interactively compare sequences, viewing the annotation data of the sequences. This system does not require installation of any programs but just a web browser that understands JavaScript.

2 FEATURES AND USAGE

The main page of the CGAS consists of the interactive comparison and annotation panes (Fig. 1A). Users may upload their BLAST outputs (Altschul et al., 1997) to the server to view the alignments between the query and the subject sequences. The server automatically generates a dot plot of the alignments. The comparison pane displays the hits between the query and a subject in a 2D representation. Annotation panes are placed along the left and the upper edges of the comparison pane. They display the annotation data of the query and the subject graphically. User-defined annotation data may be uploaded in the gbk/gbff (http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html) or the gff data format (http://www.sequenceontology.org/gff3.shtml). In the case where the sequence names in the uploaded alignment data are recognized as those defined at NCBI, the system automatically fetches the annotation data from NCBI through the TogoWS system (http://togows.dbcls.jp/).

Fig. 1.

The main page of CGAS, consisting with comparison and annotation panes. This example shows a comparison of the regions including the opsin loci in the X chromosomes of human and chimpanzee (A: single mode) and macaque (B: dual mode). Red and blue dots/lines in the comparison pane represent the BLAST hits in the same/different directions between the query and the subject.

Users can move about the entire dot plot by dragging the comparison pane and zoom it in/out with the mouse wheel in the same manner as the Google Maps. The navigation controls, placed at the upper-left corner of the comparison pane, may be used to navigate. Diagonal movements are possible using the navigation controls. Thanks to the Google Maps API, the annotation panes are updated synchronously with the comparison pane.

The names of the annotated objects are shown in a small box, which can be expanded by moving the mouse cursor on it and shows annotation details along with the link to the original data at NCBI. If the mouse cursor is within the comparison pane, the position of the cursor in each of the query and the subject(s) is indicated by a red thin line in the annotation pane with the position information in base pairs. The current version of CGAS is capable of displaying two subjects side by side (Fig. 1B). Two comparison panes are synchronously aligned to the query. This functionality allows the users to compare the differences in collinearity between the subjects.

CGAS provides a unique function to align the query and the subject annotation panes based on the putative orthology relationships between the sequences compared. If the user double-clicks in the subject or query panes, the most similar region of the clicked region in the query or subject sequence is centered in the pane, and the comparison pane is updated accordingly. This is useful for tracking the significant hits.

The uploaded data are indexed with user's login ID and retained in the server for a week after the last access or until the user deletes them.

3 IMPLEMENTATION

The CGAS is a web server with the Ruby on Rails framework with JavaScript. The interface within the dot plot viewer and the annotation viewer was implemented using Google Maps API version 2. Interpretation of biological data and interactive entry fetching from public database were achieved by the BioRuby library (http://bioruby.org/) and the TogoWS system. The documentation of CGAS is provided at http://cgas.ist.hokudai.ac.jp/help/.