GeneSeqer is a gene identification tool based on spliced alignment or “spliced threading” of ESTs with a genomic query sequence. In a spliced alignment, aligned residues in the genomic sequence are assigned exon status. Introns are identfied as large gaps in the alignment, typically (but not necessarily) flanked by the consensus GT and AG dinucleotides at the donor and acceptor sites, respectively. The optimal alignment is derived by scoring for both sequence similarity and potential splice site strength. The program is designed to handle alignment of a large number of ESTs on a long genomic query sequence (BAC size). Therefore, the ESTs are pre-screened, and only ESTs with sufficient significant matching are fully aligned.
The Brendel Group @ Indiana University
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Brendel, V., Xing, L. and Zhu, W.
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
Bioinformatics 20(7), 1157-1169 (2004).