The NCBI is now distributing the BLAST databases for protein PDB (pdbaa) and Swiss-Prot (swissprot) as stand-alone BLAST databases, rather than as subsets of the non-redundant (nr) database. This change means that the pdbaa and swissprot databases can now be used independently of the nr database. This change does require users to first remove all existing swissprot and pdbaa alias files and mask files. On a UNIX/LINUX system this can be accomplished by executing the command below.
rm –f swissprot.*.pal swissprot.*.msk pdbaa.*.pal pdbaa.*.msk
