Nucleic Acids Research, 2004, Vol. 32, Database issue D59-D63
© 2004 Oxford University Press
Xpro: database of eukaryotic protein-encoding genes
1 Department of Biochemistry and 2 Department of Biological Sciences, National University of Singapore, Singapore 119260
*To whom correspondence should be addressed. Tel: +65 6874 3566; Fax: +65 6778 2466; Email: shoba{at}bic.nus.edu.sg
Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture. In addition to the information found in the GenBank records, which includes properties such as sequence, position, length and description about introns, exons and protein-coding regions, Xpro provides annotations on the splice sites and intron phases. Furthermore, Xpro validates intron positions using alignment information between the record’s sequence and EST sequences found in dbEST. In the process of validation, alternative splicing information is also obtained and can be found in the database. The intron-containing genes in the Xpro are also classified as experimental or predicted based on the intron position validation and specific keywords in the GenBank records that are present in predicted genes. An Entrez-like query system, which is familiar to most biologists, is provided for accessing the information present in the database system. A non-redundant set of Xpro database contents is also obtained by cross-referencing to the Swiss-Prot/TrEMBL and Pfam databases. The database currently contains information for 493 983 genes—351 918 intron- containing genes and 142 065 intron-less genes. Xpro is updated for each new GenBank release and is freely available via the internet at http://origin.bic. nus.edu.sg/xpro.
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