Blast databases available locally
Many pipelines involving annotation/assembly comparison involve Blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Several Blast versions are available as modules, for example:
- blast/2.7.1+, etc. : the Blast+ suites (
tblastn, etc.), recommended
- blast/2.2.26, etc. : 'legacy' Blast (
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 those available at NCBI (ftp://ftp.ncbi.nih.gov/blast/db/README) as well as several UniProt databases (http://www.uniprot.org/). Note that:
- The local copies are found at
- 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_oldis deleted the second data of each month at 00.01
The databases available are:
|cdd_delta||protein||NCBI||Conserved domain database for use with
|env_nr||protein||NCBI||Protein sequences for metagenomes (EXCLUDED from nr)|
|env_nt||nucleotide||NCBI||Nucleotide sequences for metagenomes|
|human_genomic||nucleotide||NCBI||Human RefSeq chromosome records|
|nr||protein||NCBI||Non-redundant protein sequences|
|nt||nucleotide||NCBI||Partially non-redundant nucleotide sequences|
|other_genomic||nucleotide||NCBI||RefSeq chromosome records for non-human organisms|
|pataa||protein||NCBI||Sequences for protein structures from patents (EXCLUDED from nr)|
|patnt||nucleotide||NCBI||Nucleotide sequences for pataa protein structures from patents|
|pdbaa||protein||NCBI||Sequences for protein structures from Protein Data Bank|
|pdbnt||nucleitide||NCBI||Nucleotide sequences for pdbaa protein structures from Protein Data Bank|
|refseq_genomic||nucleotide||NCBI||NCBI genomic reference sequences|
|refseq_protein||protein||NCBI||NCBI protein reference sequences|
|refseq_rna||nucleotide||NCBI||NCBI Transcript reference sequences|
|swissprot||protein||NCBI||Swiss-Prot sequence 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|
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.
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, TSA and SRA sequence databases are not included
The NCBI Whole-Genome Shotgun is no longer downloaded locally. NCBI provides special versions of Blast and other tools that can be used to search the remote versions of WGS, the Transcriptome Shotgun Assembly, 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 TSA identifiers.