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, 22 (6), 495-503

Identification of Minimal Eukaryotic Introns Through GeneBase, a User-Friendly Tool for Parsing the NCBI Gene Databank

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Identification of Minimal Eukaryotic Introns Through GeneBase, a User-Friendly Tool for Parsing the NCBI Gene Databank

Allison Piovesan et al. DNA Res.

Abstract

We have developed GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, which generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers. Features of all the annotated eukaryotic genes are accessible through three main software tables, including for each entry details such as the gene summary, the gene exon/intron structure and the specific Gene Ontology attributions. The structuring of the data, the creation of additional calculation fields and the integration with nucleotide sequences allow users to make many types of comparisons and calculations that are useful for data retrieval and analysis. We provide an original example analysis of the existing introns across all the available species, through which the classic biological problem of the 'minimal intron' may find a solution using available data. Based on all currently available data, we can define the shortest known eukaryotic GT-AG intron length, setting the physical limit at the 30 base pair intron belonging to the human MST1L gene. This 'model intron' will shed light on the minimal requirement elements of recognition used for conventional splicing functioning. Remarkably, this size is indeed consistent with the sum of the splicing consensus sequence lengths.

Keywords: NCBI Gene; computational biology; gene data parsing; minimal intron; personal computer software.

Figures

Figure 1.
Figure 1.
Flow diagram illustrating the data parsing involved in the GeneBase development. ‘Gene_Summary’, ‘Gene_Table’ and ‘Gene_Ontology’ are the three main related software tables.
Figure 2.
Figure 2.
Screen shot of GeneBase ‘Gene_Table’ interface. Fields are described in detail in the software documentation. Exon and coding exon sequences are in distinct fields to allow an independent management of data (see Materials and methods). This figure is available in black and white in print and in colour at DNA Research online.

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References

    1. Smith T.F. 1990, The history of the genetic sequence databases, Genomics, 6, 701–7. - PubMed
    1. Kennard O. 1997, From private data to public knowledge. In: Butterworth I., editor. , (ed.), The Impact of Electronic Publishing on the Academic Community, an International Workshop Organised by the Academia Europaea and the Wenner-Gren Foundation, Wenner-Gren Center, Stockholm, 16–20 April, 1997 Portland Press Ltd, London, UK.
    1. Brown G.R., Hem V., Katz K.S. et al. 2014, Gene: a gene-centered information resource at NCBI, Nucleic Acids Res., 43, D36–42. - PMC - PubMed
    1. Lewitter F. 1998, Text-based database searching, TRENDS Biotechnol., 16, 3–5.
    1. Hart K.W., Searls D.B., Overton G.C. 1994, SORTEZ: a relational translator for NCBI's ASN.1 database, Comput. Appl. Biosci., 10, 369–78. - PubMed

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