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

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 alignm...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante, Maria Luisa Chiusano
• Keywords: Ab Initio, BMCBI 2007, Candidate Gene Models, Gene Models