EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis

EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases fr om multiple external sources. The information in EpoDB obtained from GenBan k, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality d ata for sequence analysis aimed at understanding gene regulation during ery thropoiesis, New protocols have been developed for data integration and upd ating entries. Using a BLAST-based algorithm, we have grouped GenBank entri es representing the same gene together, This sequence similarity protocol w as also used to identify new entries to be included in EpoDB. We have recen tly implemented our database in Sybase (relational tables) in addition to S ICStus Prolog to provide us with greater flexibility in asking complex quer ies that utilize information from multiple sources. New additions to the pu blic web site (http://www.cbil.upenn.edu/epodb) for accessing EpoDB are the ability to retrieve groups of entries representing different variants of t he same gene and to retrieve gene expression data. The BLAST query has been enhanced by incorporating BLAST-View, an interactive and graphical display of BLAST results. We have also enhanced the queries for retrieving sequenc e from specified genes by the addition of MEME, a motif discovery tool, to the integrated analysis tools which include CLUSTALW and TESS.