i started working on est assembly and annotation of a plant species some months back, till that time complete genome sequence was not available. Now the species has its genome sequence sequenced and annotated and is in list of refgenomes. By the time i also finished EST pre-processing and assembly. Now can i still use my EST assembly data for gene finding (in the species genome sequence itself) so as to find some additional information as the genome has been annotated using homology based searches and ab initio methods? will it be relevant? can i go for mapping of est contigs and singletons on the genome, if yes what are tools available for this.
PASA was one of the first, if not the first, EST assembly programs that existed long before RNA-Seq was in vogue. You splice-align transcripts using a program like GeneSeqer, and then PASA assembles the alignments. I haven't personally used it for annotation, but in its documentation PASA brands itself as an annotation tool.