NAR Molecular Biology Database Collection entry number 450

http://eased.bioinf.mdc-berlin.de/

Pospisil H.^1,2, Herrmann A.², Reich J.²

¹Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
²Max-Delbrueck-Center for Molecular Medicine Berlin, R.-Roessle-Str. 10, 13125 Berlin, Germany

Contact pospisil@zbh.uni-hamburg.de

EASED is a database of predicted alternative splice forms (ASforms). ASforms are defined by comparing high-scoring ESTs with mRNA sequences using BLAST, taking known exon-intron information (from the ENSEMBL database). Filtering programs compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which indicate the existence of alternative splice forms with respect to the exon-intron boundaries. Moreover, we defined the alternative splice profile of each sequence. It indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE correspond to the EST coverage and can be used as a quality indicator for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene.

Additionally, the tissue type information of all ESTs was included. This allows (a) restriction of the search to certain tissues and (b) calculation of the tissue-NAEs, tissue-NCEs and tissue-NSS. These scores are suitable for the estimation of tissue specificity of certain ASforms. Furthermore, the developmental stage and disease information of the ESTs is available. EASED is accessible at http://www.bioinf.mdc-berlin.de/splice/db/

The database of alternatively spliced ESTs was completed for some more organisms (the available organisms from the ENSEMBL database). Moreover, we updated our tissue catalogue using a DAG that is based on the MeSH tree. The updated graphical representation allows a better distinguishing of the tissue classes. As an additional advantage, all found splice sites for an ASforms query we grouped with respect to the belonging genes. Furthermore, the number of different libraries can be comprised as a quality check for alternative splice sites.

This work was supported by a grant from the Federal Ministry of Education and Research (01SF9988/4)

Go to the abstract in the NAR 2004 Database Issue.

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