Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

Erdahl T Teber¹^,4^,5 , Edward Crawford¹ , Kent B Bolton² , Derek Van Dyk³ , Peter R Schofield⁴^,6 , Vimal Kapoor¹^,7 and W Bret Church¹^,4^,5

¹School of Medical Sciences, University of New South Wales NSW 2052, Australia

²EBM Pty Ltd, Level 6, 110 Sussex Street, Sydney, NSW 2000, Australia

³NSW Ministry for Science and Medical Research, GPO Box 5341, Sydney NSW 2001, Australia

⁴Neurobiology Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia

⁵Faculty of Pharmacy, University of Sydney NSW 2006, Australia

⁶Prince of Wales Medical Research Institute, Sydney NSW 2031, Australia

⁷Department of Medicine and Pharmacology, University of Western Australia, Crawley WA 6009, Australia

author email corresponding author email

BMC Bioinformatics 2006, 7:33doi:10.1186/1471-2105-7-33


Published:	23 January 2006

Abstract

Background

There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences.

Results

Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant.

Conclusion

Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence annotations relating to a gene, its transcripts and translations. The mechanism of transcript definition and creation, and subsequent navigation and exploration of features, are very intuitive and demand only a short learning curve. Ultimately, Djinn Lite can form the basis for providing valuable clues to plan new experiments, providing storage of sequences and annotations for dedication to customised projects. The application is appropriate for Windows 98-ME-2000-XP-2003 operating systems.