This might look like a very basic question but I would appreciate any assistance since I am not well grounded in bioinformatics. I have several whole genome sequences of a species of my interest (Oryza sp.). I need to extract sequences of certain genes from these genomes and then identify variations in these genes among the various samples that I have. To extract the sequences, I need to download sequences of my genes of interest so that they can act as my reference. Sequences of my genes of interest are in gramene database and are well annotated (in terms of CDS, intron, exon etc.). My problem is that I am unable to download the sequences with the annotations (I can download sequences without annotations). I need the annotations so as to know which variations fall in coding, non coding regions etc. I have successfully done this kind of download from GenBank but not gramene. Any help will be appreciated!
