ASPicDB:: A database resource for alternative splicing analysis
ASPicDB:: A database resource for alternative splicing analysis
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DOI：
10.1093/bioinformatics/btn113
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发表时间：
2008-05-15
期刊：
影响因子：
5.8
通讯作者：
Pesole, G.
中科院分区：
文献类型：
--
作者：
Castrignano, T.;D'Antonio, M.;Pesole, G.
动机：选择性剪接最近已经成为导致人类和其他生物中转录组和蛋白质组复杂性扩大的关键机制。虽然有几个专门用于替代剪接分析的在线资源，但它们可能会受到与所采用的计算方法以及它们所提供的注释的范围有关的限制，这些注释妨碍了对现有数据的充分利用。此外，现有资源提供的查询和下载功能有限。结果：ASPicDB是一个数据库，旨在提供对人类基因选择性剪接模式的可靠注释和预测剪接异构体的功能注释。基于基因相关转录本(通常是Unigene簇)与基因组序列的多重比对，基于ASPIC算法的全基因组应用，剪接点检测和全长转录本建模已经被执行，与基于独立和递进比对的方法相比，这一策略大大提高了预测精度。增强的注释和序列的查询和下载工具允许用户选择和提取与满足用户定义的标准组合的基因、转录本和内含子相关的特定数据集。ASPicDB每月定期更新，还包括基于可用的EST序列及其文库来源注释的正常细胞和癌细胞的组织特异性剪接模式的信息。
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.