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BMCBI
2007

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

14 years 3 days ago
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...
Nunzio D'Agostino, Alessandra Traini, Luigi Frusci
Added 12 Dec 2010
Updated 12 Dec 2010
Type Journal
Year 2007
Where BMCBI
Authors Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante, Maria Luisa Chiusano
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