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Usage

BLASTDB Location

All databases are located in /data/reference/blast/db. The default database directory is a symlink to the latest release, but the older releases are still available. Its location is set automatically by the ncbi_blast module via the $BLASTDB environment variable. To override the default database location to perhaps use an older release or your own directory run export BLASTDB=/some/path either on the command line or in the job script as appropriate. E.g. export BLASTDB=/data/reference/blast/201506. Afterwards, continue calling databases by name without the full path. For example, blastx -db nr ....

Hosted BLAST Databases

NCBI Databases

We periodically mirror the entire NCBI BLAST reference databases. Below is a list of the current BLAST databases, please note this list is to subject to change with updates.

  • 28S_fungal_sequences
  • 16S_ribosomal_RNA
  • ITS_RefSeq_Fungi
  • Betacoronavirus
  • 18S_fungal_sequences
  • ITS_eukaryote_sequences
  • LSU_eukaryote_rRNA
  • LSU_prokaryote_rRNA
  • SSU_eukaryote_rRNA
  • env_nt
  • env_nr
  • human_genome
  • landmark
  • mito
  • mouse_genome
  • nr
  • nt_euk
  • nt
  • nt_others
  • nt_prok
  • nt_viruses
  • pataa
  • patnt
  • pdbaa
  • pdbnt
  • ref_euk_rep_genomes
  • ref_prok_rep_genomes
  • ref_viroids_rep_genomes
  • ref_viruses_rep_genomes
  • refseq_select_rna
  • refseq_select_prot
  • refseq_protein
  • refseq_rna
  • swissprot
  • tsa_nr
  • tsa_nt
  • taxdb
  • core_nt

Custom Databases

We can also build custom databases upon request. As an added benefit, when we host a custom database and make it available to all HiPerGator users; it won't consume your group's blue quota. Please submit a support request for more information.

  • Alligator.miss.v0.2 - Alligator mississippiensis v. 0.2 build
  • aliivibrio_fischeri - Aliivibrio Fischeri (ASM1180v1)
  • a_baumannii-AB0057 - A. baumannii str. AB0057
  • aplCal3 - A. californica 3.0 WGS assembly, 4331 contigs
  • a_thaliana_tair10_ufrc
  • baciSubt
  • camelus_dromedarius_ufrc - Camelus Dromedarius` - JDVD01000001.1
  • CFSAN001992_ufrc
  • chlaCavGPIC - Chlamydia psittaci (GPIC)
  • chlaPneumAR39 - Chlamydia Pneumoniae
  • chlaTracA - Chlamydia trachomatis serovar A
  • chlaTracD - Chlamydia trachomatis serovar D
  • chlaTracL2 - Chlamydia trachomatis serovar L2
  • chlaTracMurNigg - Chlamydia muridarum
  • cp003200_1_ufrc
  • cp012090_ufrc
  • danio_rerio_grcz10_ufrc
  • danio_rerio_zv9_75_rm_toplevel_ufrc
  • Danio Rerio (GRCZ10)
  • Danio Rerio (zv9)
  • daphnia_pulex_all
  • dmel-r6
  • DROME_prot - Deep Metazoan Project protein database
  • e_faecalis_GCA_000172575
  • Escherichia_coli
  • eucalyptus_grandis_2
  • Eucalyptus Grandis - Eucalyptus Grandis v2.0
  • fa_fb_1
  • fa_rr_1
  • GCF_000001405
  • GCF_000001635
  • GCF_000007585
  • grch38
  • GRCh38.p11 - Human Genome assembly GRCh38.p11
  • hg18
  • hg19
  • hhv8gk18
  • hhv8jsc1
  • klebsiella_pneumoniae_CAV1596
  • Klebsiella Pneumoniae (CAV1596)
  • Klebsiella Pneumoniae (HS11286)
  • Klebsiella Pneumoniae (MGH78578)
  • Klebsiella_pneumoniae_CAV1596-97
  • klebsiella_pneumoniae_mgh_78578_ufrc
  • lsu108 - LSURef
  • lsu111 - LSURef
  • LSUParc_115 - [1]
  • LSURef_115 - [2]
  • md5nr - A comprehensive non-redundant protein database
  • MHV4_NC_001826_2
  • mm10
  • mm9
  • MRSAplasmids2014
  • m_tuberculosis-CDC1551 - M. tuberculosis str CDC1551
  • m_tuberculosis_H37Rv_ufrc
  • musa_acuminata_v2_ufrc
  • n_meningitides_cfam18
  • n_meningitidis_serB_MC58
  • Oreochromis_niloticus_oreNil2_ufrc
  • oryx_leucoryx_ufrc - Oryx Leucoryx - oryxL1s1
  • Phum_Geneious_A
  • Phum_Geneious_B
  • PhumU1_USDA_sc - Pediculus humanus USDA suupercontigs
  • Phytophthora_parasitica_ufrc
  • p_schaeffi_v0_1_bboyd - Bret Boyd's build
  • p_tremula_alba_717_v1
  • P Tremula x Alba 717-1B4 v1.1
  • p_trichocarpa_v3_0
  • rfam_10_1 - release 10.1
  • rfam_11 - release 11
  • rn5 - Ratticus norvegicus rn5 release
  • rn6_draft_73_sm
  • Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992
  • salmTyph14028S
  • s_aureus
  • s_bicolor_v2
  • s_enterica
  • shigella_flexneri_2a_2457T_ufrc
  • shigella_phage_POCJ13_ufrc
  • Silba_123_SSURef
  • Silva_128_ss_nr99_ufrc
  • s_mutans-UA159-NC_004350
  • Solanum_pimpinellifolium_ufrc
  • Sorbi1
  • Sorbi1.21
  • ssu108nr - SSURef NR
  • ssu111nr - SSURef NR
  • SSUParc_115 - [3]
  • SSURef_NR99_115 - [4]
  • taxonomy4blast
  • t_manatus_29620
  • vcarteri_317_v2
  • v_cholerae_o1_2010el_1786
  • vibrChol1 - Vibrio cholerae O1 biovar eltor str. N16961
  • vibrChol_O395_1 - Vibrio cholerae O395
  • Vibrio_phage_CTX_HQ224500
  • vibrVuln_CMCP6_1 - Vibrio vulnificus CMCP6
  • x_perforans
  • zea_mays
  • zea_mays_AGPv4_ensembl_ufrc
  • zea_mays_AGPv4_sm_enseml_ufrc
  • zika_kx_922705_ufrc
  • ZmB73_RefGen_v2_ufrc