I have a interested gene A which sequence information have been cloned and experssion patterns have been analyzed in species A, while I can't find (through BLAT and BLAST) any hits in gene models of species A (whose whole genome have been sequenced). So I inferred that this mismatch may be for some missing of species A genome annotation, and I wanted to re-annotate regions of species A genome which are relative to gene A (or correspondent gene family). My ideas about this re-annotation pathway was shown as follows:
1). Extract special region from assembly file of species A. In this step, my question is how to extract this region, and if we need to extend 1kb at the 5' and 3' end of this region.
2). Using Fgenesh and Augustus to ab inito predict genes of this region.
3). Using exonerate to map cDNA and protein (homology sequences of gene A) to this region.
4). Using EVM to combine all genes, and then produce gff file.
As a newer, I don't know if my pathway is correct. If you have any suggestions, please tell me.