Adding BLAST Databases
|April 22, 2017|
The [+]/[-] indicators in the Add menu will not be updated
to reflect addition of new databases until the next time
you launch birchadmin after the download is completed.
|At the command line - Suppose you
wanted to add
vector and Taxonomy databases:
blastdbkit.py --add --dblist swissprot,vector,taxdb
blastdbkit --add --dblist all
Adds ALL databases from the remote FTP site. At this writing, that corresponds to about 850 Gb!
notes on est and pdbnt databases
Reference: BLAST FTP Site
The est and pdbnt databases do not themselves contain sequences. Rather, they contain IDs of sequences in other databases.
est - Contains ACCESSION numbers for sequences in the est_human, est_mouse and est_others databases. In practice, the est database is a virtual database containing the union of those three databases.
pdbnt - Contains ACCESSION numbers for only those sequences in the nt database that for which a 3D structure is found in PDB. Example: 1C2W_B - Chain B, 23s Rrna Structure Fitted To A Cryo-Electron Microscopic
When BLAST searches est or pdbnt, the search is redirected to the component databases. A search of searches est_human, est_mouse and est_others. A search of pdb searches only those sequences in the nt database that also have a structure in PDB.
>>> If you install est, you MUST also install est_human, est_mouse and est_others.
>>> If you install pdbnt, you MUST also install nt.