MAASE: an alternative splicing database designed for supporting splicing microarray applications

Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequ...

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Bibliographic Details
Published in:RNA (Cambridge) 2005-12, Vol.11 (12), p.1767-1776
Main Authors: Zheng, Christina L, Kwon, Young-Soo, Li, Hai-Ri, Zhang, Kui, Coutinho-Mansfield, Gabriela, Yang, Canzhu, Nair, T Murlidharan, Gribskov, Michael, Fu, Xiang-Dong
Format: Article
Language:English
Subjects:
Alternative Splicing
Bioinformatics
Computational Biology
Database Management Systems
Databases, Genetic
Genome
Microarray Analysis
RNA Splicing
RNA, Messenger - chemistry
User-Computer Interface
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Summary:Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequence information, is a promising approach. Despite the availability of a large number of mRNAs and ESTs in various databases and the efforts made to align transcript sequences to genomic sequences, existing alternative splicing databases do not offer adequate information in an appropriate format to aid in splicing array design. Here we describe our effort in constructing the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is specifically designed to support splicing microarray applications. MAASE comprises two components: (1) a manual/computational annotation tool for the efficient extraction of critical sequence and functional information for alternative splicing events and (2) a user-friendly database of annotated events that allows convenient export of information to aid in microarray design and data analysis. We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication.
ISSN:1355-8382
1469-9001
DOI:10.1261/rna.2650905