University of Connecticut University of UC Title Fallback Connecticut

Databases

The following NCBI BLAST databases are updated on a weekly basis and available to users with an account on the cluster.  Older versions are not maintained but if you require a specific version of a database or one not listed here, please contact us.

All databases listed are current as of 03/14/2017

NCBI BLAST Databases

Database Type Path on Server Description
nt Nucleic /common/blast/data Nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ excluding bulk divisions (gss, sts, pat, est, and htg divisions. wgs entries are also excluded. Not non-redundant.
nr Protein /common/blast/data Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq
swissprot Protein /common/blast/data Swiss-prot sequence databases (last major update), it’s parent database is nr.
env_nt Nucleic /common/blast/data Nucleotide sequences for metagenome
env_nr Protein /common/blast/data Nucleotide sequences for metagenome
tsa_nt Nucleic /common/blast/data Sequences from the TSA division of GenBank, EMBL, and DDBJ
16SMicrobial Nucleic /common/blast/data Bacterial and Archaeal 16S rRNA sequences from BioProjects 33175 and 33117
refseq_rna Nucleic /common/blast/data NCBI Transcript reference sequences
refseq_protein Protein /common/blast/data NCBI protein reference sequences.
refseq_genomic Nucleic /common/blast/data NCBI genomic reference sequences
taxdb Phylogeny /common/blast/data Taxonomy
cdd_delta Nucleic /common/blast/data Conserved Domain Database sequences for use with stand alone deltablast

NCBI Diamond Databases

Database Type Path on Server Description
nt_nucleotide.dmnd Nucleic /common/Diamond/ntnr Nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ excluding bulk divisions (gss, sts, pat, est, and htg divisions. wgs entries are also excluded. Not non-redundant.
nr_protein.dmnd Protein /common/Diamond/ntnr Non-redundant protein squence database with entries from GenPept, Swissprot, PIR, PDF, PDB and NCBI RefSeq
complete.rna.fna.dmnd Nucleic /common/Diamond/RefSeq NCBI Transcript reference sequences
complete.protein.faa.dmnd Protein /common/Diamond/RefSeq NCBI protein reference sequences.
plant.protein.faa.dmnd Protein /common/Diamond/RefSeq NCBI plant protein reference sequences

Plant Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Amborella trichopoda (shrub) 1.0 Phytozome  /common/data/Atrichopoda/v1.0/Star
/common/data/Atrichopoda/v1.0/Bowtie
/common/data/Atrichopoda/v1.0/Gmap
Arabidopsis halleri (rockcress) 1.1 Phytozome /common/data/Arabidopsis/halleri/Ahalleri_STAR
/common/data/Arabidopsis/halleri/Ahalleri_bowtie2
/common/data/Arabidopsis/halleri/Ahalleri_gmap
Arabidopsis lyrata 1.0 Phytozome /common/data/Arabidopsis/lyrata/Alyrata_STAR/
/common/data/Arabidopsis/lyrata/Alyrata_bowtie2
/common/data/Arabidopsis/lyrata/Alyrata_gmap
Arabidopsis thaliana (thale cress) 10 Phytozome /common/data/Arabidopsis/thaliana/Athaliana_STAR
/common/data/Arabidopsis/thaliana/Athaliana_bowtie2
/common/data/Arabidopsis/thaliana/Athaliana_gmap
Cucumis sativus (cucumber) 1.0 Phytozome  /common/data/Csativus/v1.0/Bowtie
/common/data/Csativus/v1.0/Star
/common/data/Csativus/v1.0/Gmap
Glycine max (soybean) 1.1 Phytozome  /common/data/Gmax/v1.1/Bowtie
/common/data/Gmax/v1.1/Star
/common/data/Gmax/v1.1/Gmap
Mimulus guttatus (monkeyflower) 2.0 Phytozome  /common/data/Mguttatus/v2.0/bowtie
/common/data/Mguttatus/v2.0/Gmap
/common/data/Mguttatus/v2.0/Star
Oryza sativa (rice) 7.0 Phytozome  /common/data/Osativa/v7.0/Bowtie
/common/data/Osativa/v7.0/Gmap
/common/data/Osativa/v7.0/Star
Physcomitrella patens (moss)  3.0 Phytozome /common/data/physcomitrella3.0/Platens3.0_STAR
/common/data/physcomitrella3.0/Ppatens3.0_bowtie2
/common/data/physcomitrella3.0/Ppatens3.0_gmap
Physcomitrella patens (moss)  3.3 Phytozome /common/data/physcomitrella3.3/Platens3.3_STAR
/common/data/physcomitrella3.3/Ppatens3.3_bowtie2
/common/data/physcomitrella3.3/Ppatens3.3_gmap
Prunus persica 2.1 Phytozome  /common/data/Ppersica/v2.1/bowtie2
/common/data/Ppersica/v2.1/Gmap
/common/data/Ppersica/v2.1/Star
Populus trichocarpa (black cottonwood) 3.0 Phytozome /common/data/Ptrichocarpa_v3/Ptrichocarpa_STAR
/common/data/Ptrichocarpa_v3/Ptrichocarpa_bowtie2
/common/data/Ptrichocarpa_v3/Ptrichocarpa_gmap
Salix purpurea (shrub willow) 1.0 Phytozome  /common/data/Spurpurea/v1.0/Bowtie
/common/data/Spurpurea/v1.0/Gmap
/common/data/Spurpurea/v1.0/Star
Sorghum bicolor (cereal grass) 3.1 Phytozome  /common/data/Sbicolor/v3.1/Bowtie
/common/data/Sbicolor/v3.1/Gmap
/common/data/Sbicolor/v3.1/Star
Vitis vinifera (grape vine) Genoscope.12X Phytozome  /common/data/Vvinifera/Genoscope.12X/Bowtie
/common/data/Vvinifera/Genoscope.12X/Gmap
/common/data/Vvinifera/Genoscope.12X/Star
Zea mays (maize) 5b Phytozome  /common/data/Zmays/5b/Bowtie
/common/data/Zmays/5b/Gmap
/common/data/Zmays/5b/Star

Animal Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Bos taurus (cattle) 3.1 Ensembl /common/data/cow/cow_STAR
/common/data/cow/cow_bowtie2
/common/data/cow/cow_gmap
Canis lupus familiaris (dog) Ensembl  /common/data/CFamiliaris/bowtie2
/common/data/CFamiliaris/Gmap
/common/data/CFamiliaris/Star
Danio rerio (zebrafish) GRCz10 – R81 Ensembl /common/data/zebrafish/zebrafish_STAR
/common/data/zebrafish/zebrafish_bowtie2
/common/data/zebrafish/zebrafish_gmap
Dasypus novemcinctus (armadillo) Enzembl  /common/data/DNovemcinctus/bowtie2
/common/data/DNovemcinctus/Gmap
/common/data/DNovemcinctus/Star
Drosophila melanogaster (fruitfly) 6.0 NCBI /common/data/dm6/dm6_STAR
/common/data/dm6/dm6_bowtie2
/common/data/dm6/dm6_gmap
Felis catus (cat) Ensembl  /common/data/FCatus/bowtie2
/common/data/FCatus/Gmap
/common/data/FCatus/Star
Gallus gallus (chicken) Galgal4 -R81 Ensembl /common/data/chicken/chicken_STAR
/common/data/chicken/chicken_bowtie2
/common/data/chicken/chicken_gmap
Gasterosteus aculeatus (stickleback) Ensembl  /common/data/GAculeatus/bowtie2
/common/data/GAculeatus/Gmap
/common/data/GAculeatus/Star
Homo sapiens (human) GRCh38 UCSC /common/data/hg38_ucsc/hg38_STAR
/common/data/hg38_ucsc/hg38_bowtie2
/common/data/hg38_ucsc/hg38_gmap
GRCh37 UCSC /common/data/hg19_ucsc/hg19_STAR
/common/data/hg19_ucsc/hg19_bowtie2
/common/data/hg19_ucsc/hg19_gmap
Loxodonta africana (elephant) Ensembl  /common/data/LAfricana/bowtie2
/common/data/LAfricana/Gmap
/common/data/LAfricana/Star
Macaca mulatta (macaque) Ensembl  /common/data/MMulatta/bowtie2
/common/data/MMulatta/Gmap
/common/data/MMulatta/Star
Macropus eugenii (wallaby) Ensembl  /common/data/MEugenii/bowtie2
/common/data/MEugenii/Gmap
/common/data/MEugenii/Star
Mus musculus (mouse) GRCh38 – R81 Ensembl /common/data/mouse/mouse_STAR
/common/data/mouse/mouse_bowtie2
/common/data/mouse/mouse_gmap
Ovis aries (sheep) v3.1 3.1 Ensembl /common/data/sheep3.1/sheep3.1_STAR
/common/data/sheep3.1/sheep3.1_bowtie2
/common/data/sheep3.1/sheep3.1_gmap
Ovis aries (sheep) v4.0 4.0 NCBI /common/data/sheep4.0/sheep4.0_STAR
/common/data/sheep4.0/sheep4.0_bowtie2
/common/data/sheep4.0/sheep4.0_gmap
Pan troglodytes (chimpanzee) 2.1.4 Ensembl /common/data/chimpanzee/chimpanzee_STAR
/common/data/chimpanzee/chimpanzee_bowtie2
/common/data/chimpanzee/chimpanzee_gmap
Rattus norvegicus (brown rat) 6.0 Ensembl /common/data/rat/rat_STAR
/common/data/rat/rat_bowtie2
/common/data/rat/rat_gmap
Sarcophilus harrisii (tassmanian devil) Ensembl  /common/data/SHarrisii/bowtie2
/common/data/SHarrisii/Gmap
/common/data/SHarrisii/Star
Sus scrofa (pig) 10.2 Ensembl /common/data/pig/pig_STAR
/common/data/pig/pig_bowtie2
/common/data/pig/pig_gmap
Takifugu rubripes (fugu) Enzembl  /common/data/TRubripes/bowtie2
/common/data/TRubripes/Gmap
/common/data/TRubripes/Star
Xenopus tropicalis (frog) Ensembl  /common/data/Xtropicalis/bowtie2
/common/data/Xtropicalis/Gmap
/common/data/Xtropicalis/Star

Microbial Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Staphylococcus aureus NCTC 8325 Ensembl Bacteria /common/data/St_aureus/St_aureus_STAR
/common/data/St_aureus/St_aureus_bowtie2
/common/data/St_aureus/St_aureus_gmap
Streptomyces avermitilis MA-4680NBRC 14893 Ensembl Bacteria /common/data/S_avermitilis/S_avermitilis_STAR
/common/data/S_avermitilis/S_avermitilis_bowtie2
/common/data/S_avermitilis/S_avermitilis_gmap
Streptomyces coelicolor A3_2 Ensembl Bacteria /common/data/S_coelicolor/S_coelicolor_STAR
/common/data/S_coelicolor/S_coelicolor_bowtie2
/common/data/S_coelicolor/S_coelicolor_gmap

Fungal Genome Index Databases

Species Version Source Path to STAR, bowtie2, and gmap indexes
Saccharomyces cerevisiae (yeast) R64-1-1 – R82 Ensembl Bacteria /common/data/S_cerevisiae/S_cerevisiae_STAR
/common/data/S_cerevisiae/S_cerevisiae_bowtie2
/common/data/S_cerevisiae/S_cerevisiae_gmap