Scientific Databases
Blast
Blast v5 databases. For use via command-line Blast or easyblast on Biowulf| Database | Location on HPC systems | Last Updated
| Betacoronavirus | Blast v5 database: Betacoronavirus nucleotide sequence data /fdb/blastdb/Betacoronavirus | 06 May 2020 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov Human Genome GRCh38.p13 | Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28). /fdb/blastdb/GRCh38.p13 | 12 Feb 2020 |
(Updated one-time) Source: ftp.ncbi.nlm.nih.gov Human Genome GRCh38.p13 proteins | Genome Reference Consortium Human Build 38 Patch Release 13 (2019/02/28) proteins /fdb/blastdb/GRCh38.p13.prot | 12 Feb 2020 |
(Updated one-time) Source: ftp.ncbi.nlm.nih.gov IMGT | The IMGT reference directory in FASTA format is constituted by sets of immunoglobulin (IG) or T cell receptor (TR) sequences which are isolated from the IMGT reference sequences from IMGT/GENE-DB. By definition, the IMGT reference directory sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles. In the V-REGION and C-GENE exon sets, IMGT gaps have been introduced according to the IMGT unique numbering [1] [2] [3] [4]. Gene names with provisional nomenclature (with a letter S) correspond to genes not yet assigned to genomic mapped genes. They correspond to insertion/deletion polymorphism in different strains or to mutated genes. NL: Not Localized. IMGT reference sequence and gene orientation: An IMGT reference sequence for a given IG or TR gene in the IMGT reference directory in FASTA format (IMGT/GENE-DB, IMGT/V-QUEST) is provided in the 5' > 3' DNA strand orientation corresponding to the 'sense', 'plus' or 'coding strand' of that gene (DNA strand orientation). The orientation (direct or opposite) of an IG or TR gene in a given IMGT locus is given in Locus Gene order (Genomic orientation) IMGT Repertoire (IG and TR) > 1. Locus and genes > 3. Locus descriptions > Locus gene order /fdb/igblast/imgt-2022 | (Updated one-time) Source: igblast mkdir -pv imgt-2022 export PATH=$PATH: Mouse Genome (Mus Musculus) mm39 | Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) /fdb/blastdb/mm39 | 01 Jun 2021 |
(Updated one-time) Source: genome-ftp.cse.ucsc.edu Mouse Genome (Mus Musculus) mm39 Proteins | Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) Proteins /fdb/blastdb/mm39.protein | 01 Jun 2021 |
(Updated one-time) Source: www.ncbi.nlm.nih.gov Mouse Genome (Mus Musculus) mm39 RNA | Mouse genome (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) RNA sequences /fdb/blastdb/mm39.rna | 01 Jun 2021 |
(Updated one-time) Source: www.ncbi.nlm.nih.gov Mouse Genome GRCm38.p6 | Genome Reference Consortium Mouse Build 38 patch release 6 (2017/09/15) /fdb/blastdb/GRCm38.p6 | 12 Feb 2020 |
(Updated after new build release) Source: ftp.ncbi.nlm.nih.gov Mouse Genome GRCm38.p6 proteins | Genome Reference Consortium Mouse Build 38 patch release 6 (2017/09/15) proteins /fdb/blastdb/GRCm38.p6.prot | 12 Feb 2020 |
(Updated after release) Source: ftp.ncbi.nlm.nih.gov NCBI nr | NCBI nr protein v5 database for Blast 2.8.0+ onwards /fdb/blastdb/nr | 04 Mar 2020 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov NCBI nt | NCBI nucleotide nt v5 Blast database for Blast 2.8.0+ onwards /fdb/blastdb/nt | 03 Mar 2020 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov Protein Data Bank | Blast 5 database: Protein sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB. /fdb/blastdb/pdbaa | 04 Mar 2020 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov Protein Data Bank | Blast v5 database: Nucleotide sequences of experimentally determined 3D structures of biological macromolecules. More information at the PDB. /fdb/blastdb/pdbnt | 07 Dec 2019 |
(Updated weekly) Source: ftp.ncbi.nlm.nih.gov SwissProt | Swissprot Blast v5 database for Blast 2.8.0+ onwards /fdb/blastdb/swissprot | 04 Mar 2020 | (Updated weekly) Source: ftp.ncbi.nlm.nih.gov |