Castrignanò Tiziana, Rizzi Raffaella, Talamo Ivano Giuseppe, De Meo Paolo D'Onorio, Anselmo Anna, Bonizzoni Paola, Pesole Graziano
Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita' e Ricerca, CASPUR, Rome, Italy.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W440-3. doi: 10.1093/nar/gkl324.
Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus may give rise to multiple mRNAs and protein isoforms, showing both major and subtle structural variations, is an exceptionally versatile tool in the optimization of the coding capacity of the eukaryotic genome. The huge and continuously increasing number of genome and transcript sequences provides an essential information source for the computational detection of genes AS pattern. However, much of this information is not optimally or comprehensively used in gene annotation by current genome annotation pipelines. We present here a web resource implementing the ASPIC algorithm which we developed previously for the investigation of AS of user submitted genes, based on comparative analysis of available transcript and genome data from a variety of species. The ASPIC web resource provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation. The ASPIC web resource-available at http://www.caspur.it/ASPIC/--is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility.
可变剪接（Alternative splicing，AS）如今已成为一种主要机制，有助于增加多细胞生物转录组和蛋白质组的复杂性。单个基因座可能产生多个mRNA和蛋白质异构体，它们既表现出主要的结构变异，也有细微的结构变异，这一事实在优化真核基因组编码能力方面是一种极其通用的工具。数量庞大且持续增加的基因组和转录本序列为通过计算检测基因的可变剪接模式提供了重要的信息来源。然而，当前的基因组注释流程在基因注释中并未充分或全面地利用这些信息。我们在此展示一个网络资源，它实现了我们之前开发的ASPIC算法，该算法基于对来自多种物种的可用转录本和基因组数据的比较分析，用于研究用户提交基因的可变剪接。ASPIC网络资源提供了与所研究基因检测到的剪接位点兼容的所有全长mRNA异构体剪接模式的图形和表格视图，以及相关的结构和功能注释。ASPIC网络资源可通过http://www.caspur.it/ASPIC/访问，它与Ensembl和Unigene数据库动态互连，并且还具备上传功能。
