ASPicDB: A database resource for alternative splicing analysis

• Published in: Bioinformatics 2008-05, Vol.24 (10), p.1300-1304
• Main Authors: Castrignanò, T., D’Antonio, M., Anselmo, A., Carrabino, D., D’Onorio De Meo, A., D’Erchia, A. M., Licciulli, F., Mangiulli, M., Mignone, F., Pavesi, G., Picardi, E., Riva, A., Rizzi, R., Bonizzoni, P., Pesole, G.
• Format: Article
• Language: English
• Subjects: Base Sequence; Biological and medical sciences; Chromosome Mapping - methods; Computer Graphics; Database Management Systems; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; RNA Splice Sites - genetics; Sequence Alignment - methods; Sequence Analysis, DNA - methods; User-Computer Interface
• ISSN: 1367-4803; 0266-7061; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btn113

Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they provide that prevent the full exploitation of the available data. Furthermore, current resources provide limited query and download facilities. Results: ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. Splice-site detection and full-length transcript modeling have been carried out by a genome-wide application of the ASPic algorithm, based on the multiple alignments of gene-related transcripts (typically a Unigene cluster) to the genomic sequence, a strategy that greatly improves prediction accuracy compared to methods based on independent and progressive alignments. Enhanced query and download facilities for annotations and sequences allow users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB, which is regularly updated on a monthly basis, also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST sequences and their library source annotation. Availability: www.caspur.it/ASPicDB Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.