I tried to annotate a plant genome though maker, while I have no time to wait the results because of Spring Festival coming. Someone suggested that I can extract special region which is about target gene family sequences from whole genome assemble files and then annotate the extract file though augustus software.
Note: I just want to extract some sequences belong to a special gene family, but the annotation files download from genome websites is poor quality and can't be used in the further analysis. So I want to annotate the genome again.
1. I don't know how to extract special region from whole genome assemble files. If I can achieve it though BLAST or BLAT?
2. Do I need to mask the repeats of extract file of whole genome assemble files before genome annotation?
Thanks for your help!