NCBI BLAST+¶

Description¶

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s.

BLASTDB - BLAST database location

Environment Modules¶

Run module spider ncbi_blast to find out what environment modules are available for this application.

Environment Variables¶

HPC_NCBI_BLAST_DIR - installation directory
HPC_NCBI_BLAST_BIN - executable directory
HPC_NCBI_BLAST_DOC - documents directory

Additional Usage Information¶

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

Categories¶

biology