Contents of the /blast/db/ directory
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The names of these databases and their contents are listed below.

+-----------------------------+----------------------------------------------+
| File Name                   | Content Description                          |
+=============================+==============================================+
| 16SMicrobial.tar.gz         | Bacterial and Archaeal 16S rRNA sequences    |
|                             | from BioProjects 33175 and 33117             |
+-----------------------------+----------------------------------------------+
| FASTA/                      | Subdirectory for FASTA formatted sequences   |
+-----------------------------+----------------------------------------------+
| README                      | README for this subdirectory (this file)     |
+-----------------------------+----------------------------------------------+
| Representative\_Genomes.\*t | Representative bacterial/archaeal genomes    |
| ar.gz                       | database                                     |
+-----------------------------+----------------------------------------------+
| cdd\_delta.tar.gz           | Conserved Domain Database sequences for use  |
|                             | with stand alone deltablast                  |
+-----------------------------+----------------------------------------------+
| cloud/                      | Subdirectory of databases for BLAST AMI; see |
|                             | http://1.usa.gov/TJAnEt                      |
+-----------------------------+----------------------------------------------+
| env\_nr.\*tar.gz            | Protein sequences for metagenomes            |
+-----------------------------+----------------------------------------------+
| env\_nt.\*tar.gz            | Nucleotide sequences for metagenomes         |
+-----------------------------+----------------------------------------------+
| est.tar.gz                  | This file requires est\_human.\ *.tar.gz,    |
|                             | est\_mouse.*.tar.gz, and                     |
|                             | est\_others.\*.tar.gz files to function. It  |
|                             | contains the est.nal alias so that searches  |
|                             | against est (-db est) will include           |
|                             | est\_human, est\_mouse and est\_others.      |
+-----------------------------+----------------------------------------------+
| est\_human.\*.tar.gz        | Human subset of the est database from the    |
|                             | est division of GenBank, EMBL and DDBJ.      |
+-----------------------------+----------------------------------------------+
| est\_mouse.\*.tar.gz        | Mouse subset of the est databasae            |
+-----------------------------+----------------------------------------------+
| est\_others.\*.tar.gz       | Non-human and non-mouse subset of the est    |
|                             | database                                     |
+-----------------------------+----------------------------------------------+
| gss.\*tar.gz                | Sequences from the GSS division of GenBank,  |
|                             | EMBL, and DDBJ                               |
+-----------------------------+----------------------------------------------+
| htgs.\*tar.gz               | Sequences from the HTG division of GenBank,  |
|                             | EMBL, and DDBJ                               |
+-----------------------------+----------------------------------------------+
| human\_genomic.\*tar.gz     | Human RefSeq (NC\_######) chromosome records |
|                             | with gap adjusted concatenated NT\_ contigs  |
+-----------------------------+----------------------------------------------+
| nr.\*tar.gz                 | Non-redundant protein sequences from         |
|                             | GenPept, Swissprot, PIR, PDF, PDB, and NCBI  |
|                             | RefSeq                                       |
+-----------------------------+----------------------------------------------+
| nt.\*tar.gz                 | Partially non-redundant nucleotide sequences |
|                             | from all traditional divisions of GenBank,   |
|                             | EMBL, and DDBJ excluding GSS, STS, PAT, EST, |
|                             | HTG, and WGS.                                |
+-----------------------------+----------------------------------------------+
| other\_genomic.\*tar.gz     | RefSeq chromosome records (NC\_######) for   |
|                             | non-human organisms                          |
+-----------------------------+----------------------------------------------+
| pataa.\*tar.gz              | Patent protein sequences                     |
+-----------------------------+----------------------------------------------+
| patnt.\*tar.gz              | Patent nucleotide sequences. Both patent     |
|                             | databases are directly from the USPTO, or    |
|                             | from the EPO/JPO via EMBL/DDBJ               |
+-----------------------------+----------------------------------------------+
| pdbaa.\*tar.gz              | Sequences for the protein structure from the |
|                             | Protein Data Bank                            |
+-----------------------------+----------------------------------------------+
| pdbnt.\*tar.gz              | Sequences for the nucleotide structure from  |
|                             | the Protein Data Bank. They are NOT the      |
|                             | protein coding sequences for the             |
|                             | corresponding pdbaa entries.                 |
+-----------------------------+----------------------------------------------+
| refseq\_genomic.\*tar.gz    | NCBI genomic reference sequences             |
+-----------------------------+----------------------------------------------+
| refseq\_protein.\*tar.gz    | NCBI protein reference sequences             |
+-----------------------------+----------------------------------------------+
| refseq\_rna.\*tar.gz        | NCBI Transcript reference sequences          |
+-----------------------------+----------------------------------------------+
| sts.\*tar.gz                | Sequences from the STS division of GenBank,  |
|                             | EMBL, and DDBJ                               |
+-----------------------------+----------------------------------------------+
| swissprot.tar.gz            | Swiss-Prot sequence database (last major     |
|                             | update)                                      |
+-----------------------------+----------------------------------------------+
| taxdb.tar.gz                | Additional taxonomy information for the      |
|                             | databases listed here providing common and   |
|                             | scientific names                             |
+-----------------------------+----------------------------------------------+
| tsa\_nt.\*tar.gz            | Sequences from the TSA division of GenBank,  |
|                             | EMBL, and DDBJ                               |
+-----------------------------+----------------------------------------------+
| vector.tar.gz               | Vector sequences from 2010, see Note 2 in    |
|                             | section 4.                                   |
+-----------------------------+----------------------------------------------+
