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Background  The structure annotation of a genome is based either on  ab initio  methodologies or on similaritiy searches versus molecules that have been already annotated.  Ab initio  gene predictions in a genome are based on  a priori  knowledge of species-specific features of genes. The training of  ab initio  gene finders is based on the definition of a data-set of gene models. To accomplish this task the common approach is to align species-specific full length cDNA and EST sequences along the genomic sequences in order to define exon/intron structure of mRNA coding genes.    Results  GeneModelEST is the software here proposed for defining a data-set of candidate gene models using exclusively evidence derived from cDNA/EST sequences.  GeneModelEST requires the genome coordinates of the spliced-alignments of ESTs and of contigs (tentative consensus sequences) generated by an EST clustering/assembling procedure to be formatted in a General Feature Format (GFF) standard file. Moreover, the alignments of the contigs versus a protein database are required as an NCBI BLAST formatted report file.  The GeneModelEST analysis aims to i) evaluate each exon as defined from contig spliced alignments onto the genome sequence; ii) classify the contigs according to quality levels in order to select candidate gene models; iii) assign to the candidate gene models preliminary functional annotations.  We discuss the application of the proposed methodology to build a data-set of gene models of  Solanum lycopersicum , whose genome sequencing is an ongoing effort by the International Tomato Genome Sequencing Consortium.    Conclusion  The contig classification procedure used by GeneModelEST supports the detection of candidate gene models, the identification of potential alternative transcripts and it is useful to filter out ambiguous information. An automated procedure, such as the one proposed here, is fundamental to support large scale analysis in order to provide species-specific gene models, that could be useful as a training data-set for  ab initio  gene finders and/or as a reference gene list for a human curated annotation.

Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome