title: GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics.
abstract: We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a 'mean' human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/.
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy.
authors.forename: Allison
authors.initials: A
authors.lastname: Piovesan
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Caracausi
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Antonaros
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy mariachiara.pelleri2@unibo.it.
authors.forename: Maria Chiara
authors.initials: MC
authors.lastname: Pelleri
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy.
authors.forename: Lorenza
authors.initials: L
authors.lastname: Vitale
mesh_terms: D030561:Databases, Nucleic Acid; D015894:Genome, Human; D006801:Humans; D009317:National Library of Medicine (U.S.); D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014481:United States