| Abstract Detail
Bioinformatics - Afternoon Chiusano, Maria Luisa [1], D Agostino, Nunzio [1], Traini, Alessandra [1], Raimondo, Enrico [1], Aversano, Mario [1], Frusciante, Luigi [2]. An Italian Platform For Solanaceae Genomics. MOTIVATION: As partner of the Solanaceae Genomics Network, we set up a bioinformatic workbench to support the experimental annotation of the Solanum lycopersicum genome and the comparative analysis of sequence collections from other Solanaceae. The workbench as well as some relevant issues related to a large scale genomic effort are presented. Methods: Using an automated approach [1] we built two databases of ESTs from tomato and potato species downloaded from dbEST. The databases provide computationally defined transcript indices represented by singletons or tentative consensus (TC), as derived from EST clustering. The functional annotation of the expressed sequences is based on a double procedure to detect similarities with both protein and non-coding RNAs. Data are described by controlled vocabularies such as the Gene Ontologies and the Enzyme Commission numbers. The experimentally annotated BACs [2] are available by the Generic Genome Browser web interface to allow selection for reference Gene Models to test predictive approaches. The two EST databases and the GBrowse are cross-referenced and linked to the Solanaceae Genome Network resources to provide an integrated platform. Results: The platform was built to provide an Italian resource for the genomics of Solanaceae and for the International Tomato Genome Sequencing Project. The web interface of the platform can be accessed browsing genome data in the form of BAC sequences or querying the EST repositories. The possibility to investigate specific expression patterns as well as gene families may provide a relevant support for the comprehension of genome organization and functionalities. We hope that our effort represents a valuable resource for meaningful structure and functional analyses on genomic data and a reference within the Solanaceae community. [1] D’Agostino, Aversano and Chiusano, BMC Bioinformatics 2005 [2] Traini and Chiusano, SOL meeting 2006 Acknowledgements: Work supported by the Agronanotech Project (Ministry of Agriculture, Italy).
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1 - University Federico II of Naples, Structural and Functional Biology, , Italy
2 - University Federico II of Naples, Soil, Plant and Environmental Sciences, , Italy
Keywords:
Genome Annotation
EST database
expression pattern
integrated bioinformatic platform.
Session: Poster-62
Location: Ballroom CD/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 8:00 AM
Abstract ID:88 |
