ChimerDB - Database of Chimeric Sequences in the GenBank.

Kim,  Namshin; Shin,  Seokmin; Cho,  Kwang Hwi; Lee,  Sanghyuk

Genomics Inform > Volume 2(2); 2004 > Article

Original Article

Genomics & Informatics 2004;2(2): 61-66.

ChimerDB - Database of Chimeric Sequences in the GenBank.

Namshin Kim, Seokmin Shin, Kwang Hwi Cho, Sanghyuk Lee

¹Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea. sanghyuk@ewha.ac.kr
²School of Chemistry, Seoul National University, Seoul 151-747, Korea.
³Department of Bioinformatics and CAMDRC, Soongsil University, Seoul 156-743, Korea.

Abstract

Fusion proteins resulting from chimeric sequences are excellent targets for therapeutic drug development. We developed a database of chimeric sequences by examining the genomic alignment of mRNA and EST sequences in the GenBank. We identified 688 chimeric mRNA and 20,998 chimeric EST sequences. Including EST sequences greatly expands the scope of chimeric sequences even though it inevitably accompanies many artifacts. Chimeric sequences are clustered according to the ECgene ID so that the user can easily find chimeric sequences related to a specific gene. Alignments of chimeric sequences are displayed as custom tracks in the UCSC genome browser. ChimerDB, available at http://genome.ewha.ac.kr/ECgene/ChimerDB/, should be a valuable resource for finding drug targets to treat cancers.

Keywords: chimeric sequence; chromosomal translocation; trans-splicing; multi-locus transcription