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.

Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank / Piovesan, Allison; Caracausi, Maria; Ricci, Marco; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara. - In: DNA RESEARCH. - ISSN 1340-2838. - STAMPA. - 22:6(2015), pp. 495-503. [10.1093/dnares/dsv028]

Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank

PIOVESAN, ALLISON;CARACAUSI, MARIA;RICCI, MARCO;STRIPPOLI, PIERLUIGI;VITALE, LORENZA;PELLERI, MARIA CHIARA
2015

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.
2015
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank / Piovesan, Allison; Caracausi, Maria; Ricci, Marco; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara. - In: DNA RESEARCH. - ISSN 1340-2838. - STAMPA. - 22:6(2015), pp. 495-503. [10.1093/dnares/dsv028]
Piovesan, Allison; Caracausi, Maria; Ricci, Marco; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara
File in questo prodotto:
File Dimensione Formato  
Piovesan 2015 GeneBase.pdf

accesso aperto

Tipo: Versione (PDF) editoriale
Licenza: Licenza per Accesso Aperto. Creative Commons Attribuzione - Non commerciale (CCBYNC)
Dimensione 417.96 kB
Formato Adobe PDF
417.96 kB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/525969
Citazioni
  • ???jsp.display-item.citation.pmc??? 24
  • Scopus 32
  • ???jsp.display-item.citation.isi??? 33
social impact