I downloaded fasta sequences from NCBI FTP site with the method described in http://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#allcomplete . Recently, I used my customised database for blast and got many desired results. However, one thing I noticed is that some of the sequences have been updated/removed since the last time I download the whole genome dataset. And some of these removed sequences actually interfered with my results because they prevented the detection of one of my spiked-in organism. Thus, I'm wondering if there is a simple way to update my genome database using command-line tools like eDirect utils. I wish to avoid re-downloading my database at all because that's just a waste of resources.
To give an example, sequence NC_000521.3 is updated to AL844502.1 then to AL844502.2. And sequence NW_001850357.1 has been completely removed from the NCBI database.