Blast databases available locally

Many pipelines involving annotation/assembly comparison involve Blast. Several Blast versions are available as modules, for example:

  • blast/2.12.0+, etc. : the Blast+ suites (blastp, tblastn, etc.), recommended
  • diamond/2.0.14 : the DIAMOND protein aligner, recommended for protein databases. See UPPMAX's DIAMOND database webpage for more information.
  • blast/2.2.26, etc. : 'legacy' Blast (blastall, megablast, etc)

Use module spider blast to see available versions. As for all bioinformatics tools at Uppmax, module load bioinfo-tools is required before the blast modules are available.

Uppmax maintains local copies of many Blast databases, including many available at NCBI:

as well as several UniProt databases.

Note that:

  • The local UPPMAX copies are found at /sw/data/blast_databases
  • Doing module load blast_databases sets the environment variable BLASTDB to this directory; this is loaded as a prerequisite when loading any blast modules
  • New versions are installed the first day of each month at 00.01 from local copies updated the 28th of the previous month beginning at 00.01
  • When new versions are installed, the directory containing the previous versions is renamed to blast_databases_old
  • blast_databases_old is deleted the second data of each month at 00.01

These databases use the "v5" format, which includes rich taxonomic infromation with sequences, and will only work with the Blast tools from the module blast/2.8.0+ and later. Earlier module versions can still be used, but you will need to provide/build your own databases. NCBI no longer updates databases with the older "v4" databases as of February 2020, and they have been deleted from UPPMAX. The final updates of these databases (again, as of this writing nearly two years old) are available from NCBI over FTP at

Each NCBI-hosted database also includes a JSON file containing additional medatadata for that particular database. These are found in /sw/data/blast_databases/ and are named databasename*.json. The exact name varies based on the format of the database. For example, the contents of the JSON file for the nr database can be see by running

cat /sw/data/blast_databases/nr*.json

The Blast databases available at UPPMAX are:

Name Type Source Notes
16S_ribosomal_RNA nucleotide NCBI 16S ribosomal RNA (Bacteria and Archaea type strains)
18S_fungal_sequences nucleotide NCBI 18S ribosomal RNA sequences (SSU) from Fungi type and reference material (BioProject PRJNA39195)
28S_fungal_sequences nucleotide NCBI 28S ribosomal RNA sequences (LSU) from Fungi type and reference material (BioProject PRJNA51803)
Betacoronavirus nucleotide NCBI Betacoronavirus nucleotide sequences
cdd_delta protein NCBI Conserved domain database for use with delta-blast
env_nr protein NCBI Protein sequences for metagenomes (EXCLUDED from nr)
env_nt nucleotide NCBI Nucleotide sequences for metagenomes
human_genome nucleotide NCBI Current RefSeq human genome assembly with various database masking
ITS_eukaryote_sequences nucleotide NCBI Internal transcribed spacer region (ITS) for eukaryotic sequences
ITS_RefSeq_Fungi nucleotide NCBI Internal transcribed spacer region (ITS) from Fungi type and reference material (BioProject PRJNA177353)
landmark protein NCBI Proteomes of 27 model organisms. The landmark database includes complete proteomes from a few selected representative genomes spanning a wide taxonomic range, the main database used by the SmartBLAST services.
LSU_eukaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for eukaryotic sequences
LSU_prokaryote_rRNA nucleotide NCBI Large subunit ribosomal RNA sequences for prokaryotic sequences
mito nucleotide NCBI NCBI Genomic Mitochondrial Reference Sequences
mouse_genome nucleotide NCBI Current RefSeq mouse genome assembly with various database masking
nr protein NCBI Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSe
nt nucleotide NCBI Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ
pataa protein NCBI Patent protein sequences
patnt nucleotide NCBI Patent nucleotide sequences. Both patent databases are directly from the USPTO, or from the EPO/JPO via EMBL/DDBJ
pdbaa protein NCBI Sequences for the protein structure from the Protein Data Bank
pdbnt nucleitide NCBI Sequences for the nucleotide structure from the Protein Data Bank. They are NOT the protein coding sequences for the corresponding pdbaa entries.
ref_euk_rep_genomes nucleotide NCBI Refseq Representative Eukaryotic genomes (1000+ organisms)
ref_prok_rep_genomes nucleotide NCBI Refseq Representative Prokaryotic genomes (5700+ organisms)
ref_viroid_rep_genomes nucleotide NCBI Refseq Representative Viroid genomes (46 organisms)
ref_viruses_rep_genomes nucleotide NCBI Refseq Representative Virus genomes (9000+ organisms)
refseq_protein protein NCBI NCBI protein reference sequences
refseq_rna nucleotide NCBI NCBI Transcript reference sequences
refseq_select_prot protein NCBI NCBI RefSeq protein sequences from human, mouse, and prokaryotes, restricted to the RefSeq Select set of proteins. RefSeq Select includes one representative protein per protein-coding gene for human and mouse, and RefSeq proteins annotated on reference and representative genomes for prokaryotes
refseq_select_rna nucleotide NCBI NCBI RefSeq transcript sequences from human and mouse, restricted to the RefSeq Select set with one representative transcript per protein-coding gene
SSU_eukaryote_rRNA nucleotide NCBI Small subunit ribosomal RNA sequences for eukaryotic sequences
swissprot protein NCBI Swiss-Prot sequence database (last major update)
tsa_nr protein NCBI Protein sequences from the Trascriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database.
tsa_nt nucleotide NCBI A database with earlier non-project based Transcriptome Shotgun Assembly (TSA) entries. Project-based TSA entries are NOT included. Entries are EXCLUDED from the nt database.
uniprot_sprot protein UniProt Swiss-Prot high quality manually annotated and non-redundant protein sequence database
uniprot_trembl protein UniProt TrEMBL high quality but unreviewed protein sequence database
uniprot_sptrembl protein uniprot_sprot and uniprot_trembl combined
uniprot_all protein alias for uniprot_sptrembl
uniprot_all.fasta protein alias for uniprot_sptrembl
uniprot_sprot_varsplic protein UniProt UniProt canonical and isoform sequences (see link)
uniprot_uniref50 protein UniProt Clustered sets of 50%-similar protein sequences (see link)
uniprot_uniref90 protein UniProt Clustered sets of 90%-similar protein sequences (see link)
uniprot_uniref100 protein UniProt Clustered sets of identical protein sequences (see link)
UniVec nucleotide UniVec Sequences commonly attached to cDNA/genomic DNA during the cloning process
UniVec_Core nucleotide UniVec A subset of UniVec chosen to minimise false positives

Additionally, taxdb.btd and taxdb.bti are downloaded, which provide additional taxonomy information for these databases. Local copies of the NCBI Taxonomy databases are also available; further details are available on a separate page.

For UniVec and UniVec_Core, Fasta-format files containing the vector sequences are also available with the given names (e.g., /sw/data/uppnex/blast_databases/UniVec), alongside the Blast-format databases built from the same Fasta files.

The exact times all databases were updated are provided by database.timestamp files located in the directory

Databases are available automatically after loading any blast module

When any of the blast modules is loaded, the BLASTDB environment variable is set to the location of the local database copies (/sw/data/uppnex/blast_databases). The various Blast tools can use this variable to find the locations of databases, so that only the name needs to be specified.

module load bioinfo-tools blast/2.7.1+
blastp -db nr -query input.fasta

After loading the blast/2.7.1+ module, specifying blastp -db nr results in blastp searching the local copy of nr, because the BLASTDB environment variable is set when the module is loaded. Similarly, each of these would result in searching the local copy of the given database:

blastp -db pdbaa ...
blastp -db uniprot_sprot ...
blastp -db uniprot_uniref90 ...
blastn -db nt ...
blastn -db refseq_genomic ...

WGS and SRA sequence databases are not included

The NCBI Whole-Genome Shotgun is not available locally. NCBI provides special versions of Blast and other tools that can be used to search the remote versions of WGS and the Sequence Read Archive.

These special blast versions and other tools are part of NCBI's SRA Tools, which is available at Uppmax as the sratools module. We have also include auxiliary NCBI scripts in the sratools module to convert taxonomic IDs to WGS and SRA identifiers.

Note that NCBI's TSA database is available at UPPMAX, just use the database name tsa_nr or tsa_nt.

Last modified: 2022-03-18