I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by taking the sequence and using NCBI's web blast and comparing the results. Often, the results that are plant viruses on local blast turn up as plant sequence on web blast. The options are all kept the same between web blast and local blast and the only difference I can think of is that my database is about 2 months older than NCBI's. Before I download this database again, do you think this is the reason for different results? Could there be another confounding factor?