Yes. The blastdb_aliastool is a BLAST+ application that allows you to aggregate BLAST databases or create subsets from them.  When working with the traditional BLAST databases (based on GeneInfo identifiers (GIs)), you could create a subset with blastdb_aliastool by providing a GI list as your input file. We have now added support for Accession-Based BLAST databases.  We have introduced new parameters for using sequence identifiers (SeqIDs), which are accession.version identifiers in this case.  The new parameters are listed below. 

-seqid_file_in <File_In>
   Text file to convert, should contain one seq id per line
-seqid_title <String>
   Title for seqid list.
-seqid_file_out <String>
   File name of converted seq id file
-seqid_db <String>
   BLAST database for seqidlist
-seqid_dbtype <String, `nucl', `prot'>
   Molecule type BLAST database
-seqid_file_info <String>
   Display seqidlist file info
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