GBuilder--an application for the visualization and integration of EST cluster data

Abstract

This paper presents a network-centric DNA sequence visualization and analysis tool called GBuilder. The tool is an easy-to-use Java application that can be used to analyze DNA sequence clusters and assemblies. The emphasis is on the analysis of EST data, where these highly redundant collections of low-quality and often alternatively spliced or chimeric sequence data are difficult to explore. The tool has the capacity to visualize similarities or dissimilarities between sequences at the level of the nucleotide base or annotation in many ways. Sequences may also be edited manually. The novel feature of GBuilder is its ability to access different data sources and analysis applications available on the Internet and to integrate these results and functionality back into itself. External resources such as EST cluster databases and conventional command-line analysis applications are integrated and accessed using CORBA (Common Object Request Broker Architecture), which provides a standard implementation independent protocol for integration. New CORBA services can be integrated immediately if they use a known interface described using the Interface Definition Language.

Figure 1

EuroGeneIndex super cluster from the mouse EST/mRNA database (accession no. U10115). Dissimilarities between adjacent and selected sequences are highlighted. A portion from the Main window, as indicated by the rectangle, can be shown in the other window. Sequences are color coded by clone library.

Figure 2

The substring similarity between two subclusters (U10115 super cluster) is shown. The lines' colors are based on their position along the sequence. Sequences are color coded by the UniGene cluster name. Brown sequences are in UniGene cluster (Mm.3400) and green sequences are not in UniGene. The sequences may have been excluded because they are marked as low-quality sequences in dbEST (the quality annotation is shown in Fig. 3).

Figure 3

Sequences that are linked with the longest sequence (U10115 mouse EuroGeneIndex super cluster) are connected by drawing a line between them. Sequences are colored by the number of links they have to other sequences. Sequence quality annotation (measured last high quality base) is shown on top of the sequence.