MOTIVATION: Accurate gene structure annotation is a challenging computational 
problem in genomics. The best results are achieved with spliced alignment of 
full-length cDNAs or multiple expressed sequence tags (ESTs) with sufficient 
overlap to cover the entire gene. For most species, cDNA and EST collections are 
far from comprehensive. We sought to overcome this bottleneck by exploring the 
possibility of using combined EST resources from fairly diverged species that 
still share a common gene space. Previous spliced alignment tools were found 
inadequate for this task because they rely on very high sequence similarity 
between the ESTs and the genomic DNA.
RESULTS: We have developed a computer program, GeneSeqer, which is capable of 
aligning thousands of ESTs with a long genomic sequence in a reasonable amount 
of time. The algorithm is uniquely designed to tolerate a high percentage of 
mismatches and insertions or deletions in the EST relative to the genomic 
template. This feature allows use of non-cognate ESTs for gene structure 
prediction, including ESTs derived from duplicated genes and homologous genes 
from related species. The increased gene prediction sensitivity results in part 
from novel splice site prediction models that are also available as a 
stand-alone splice site prediction tool. We assessed GeneSeqer performance 
relative to a standard Arabidopsis thaliana gene set and demonstrate its utility 
for plant genome annotation. In particular, we propose that this method provides 
a timely tool for the annotation of the rice genome, using abundant ESTs from 
other cereals and plants.
AVAILABILITY: The source code is available for download at 
http://bioinformatics.iastate.edu/bioinformatics2go/gs/download.html. Web 
servers for Arabidopsis and other plant species are accessible at 
http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi and 
http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi, respectively. For non-plant 
species, use http://bioinformatics.iastate.edu/cgi-bin/gs.cgi. The splice site 
prediction tool (SplicePredictor) is distributed with the GeneSeqer code. A 
SplicePredictor web server is available at 
http://bioinformatics.iastate.edu/cgi-bin/sp.cgi