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

E.T. Teber, E. Crawford, K.B. Bolton, D. Van Dyk, P.R. Schofield, Vimal Kapoor, W.B. Church

    Research output: Contribution to journalArticle

    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 challenging task that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become more precisely 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.
    Original languageEnglish
    Pages (from-to)online - approx 5-20pp
    JournalBMC Bioinformatics
    Volume7
    DOIs
    Publication statusPublished - 2006

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    Annotation
    Data structures
    Genes
    Gene
    Modeling
    Aptitude
    Proteins
    Intuitive
    Alternate hypothesis
    Molecular Sequence Annotation
    Data Curation
    Informatics
    Learning Curve
    Protein
    Alternative Splicing
    Anniversaries and Special Events
    Proteome
    Genetic Variation
    Computational Biology
    Transcriptome

    Cite this

    Teber, E. T., Crawford, E., Bolton, K. B., Van Dyk, D., Schofield, P. R., Kapoor, V., & Church, W. B. (2006). Djinn Lite : a tool for customised gene transcript modelling, annotation-data enrichment and exploration. BMC Bioinformatics, 7, online - approx 5-20pp. https://doi.org/10.1186/1471-2105-7-33
    Teber, E.T. ; Crawford, E. ; Bolton, K.B. ; Van Dyk, D. ; Schofield, P.R. ; Kapoor, Vimal ; Church, W.B. / Djinn Lite : a tool for customised gene transcript modelling, annotation-data enrichment and exploration. In: BMC Bioinformatics. 2006 ; Vol. 7. pp. online - approx 5-20pp.
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    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 challenging task that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become more precisely 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.",
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    Teber, ET, Crawford, E, Bolton, KB, Van Dyk, D, Schofield, PR, Kapoor, V & Church, WB 2006, 'Djinn Lite : a tool for customised gene transcript modelling, annotation-data enrichment and exploration' BMC Bioinformatics, vol. 7, pp. online - approx 5-20pp. https://doi.org/10.1186/1471-2105-7-33

    Djinn Lite : a tool for customised gene transcript modelling, annotation-data enrichment and exploration. / Teber, E.T.; Crawford, E.; Bolton, K.B.; Van Dyk, D.; Schofield, P.R.; Kapoor, Vimal; Church, W.B.

    In: BMC Bioinformatics, Vol. 7, 2006, p. online - approx 5-20pp.

    Research output: Contribution to journalArticle

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    AU - Kapoor, Vimal

    AU - Church, W.B.

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    Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V et al. Djinn Lite : a tool for customised gene transcript modelling, annotation-data enrichment and exploration. BMC Bioinformatics. 2006;7:online - approx 5-20pp. https://doi.org/10.1186/1471-2105-7-33