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 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.
Zheng
Christina L
CL
Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA 92093-0651, USA.
Kwon
Young-Soo
YS
Li
Hai-Ri
HR
Zhang
Kui
K
Coutinho-Mansfield
Gabriela
G
Yang
Canzhu
C
Nair
T Murlidharan
TM
Gribskov
Michael
M
Fu
Xiang-Dong
XD
D017398:Alternative Splicing; D019295:Computational Biology; D003628:Database Management Systems; D030541:Databases, Genetic; D016678:Genome; D046228:Microarray Analysis; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry; D014584:User-Computer Interface
D012333:RNA, Messenger