دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.
المؤلفون: Teber ET; School of Medical Sciences, University of New South Wales, NSW 2052, Australia. e.teber@pharm.usyd.edu.au, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB
المصدر: BMC bioinformatics [BMC Bioinformatics] 2006 Jan 23; Vol. 7, pp. 33. Date of Electronic Publication: 2006 Jan 23.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : BioMed Central, 2000-
مواضيع طبية MeSH: Computational Biology/*methods , RNA, Messenger/*metabolism, Alternative Splicing ; Animals ; Base Sequence ; Computer Graphics ; DNA, Complementary/metabolism ; Data Interpretation, Statistical ; Database Management Systems ; Databases, Genetic ; Databases, Protein ; Exons ; Genome ; Humans ; Introns ; Molecular Sequence Data ; Proteomics/methods ; Sequence Analysis, Protein ; Sequence Homology, Nucleic Acid ; Software ; User-Computer Interface
مستخلص: 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 individualize 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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المشرفين على المادة: 0 (DNA, Complementary)
0 (RNA, Messenger)
تواريخ الأحداث: Date Created: 20060124 Date Completed: 20060525 Latest Revision: 20230415
رمز التحديث: 20240829
مُعرف محوري في PubMed: PMC1397871
DOI: 10.1186/1471-2105-7-33
PMID: 16426464
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2105
DOI:10.1186/1471-2105-7-33