We provide a set of centrally-maintained scientific reference databases for Biowulf users. You can search through this data here. To request a new database or an update, please contact us at staff@hpc.nih.gov.
| Search by keyword | Searches through metadata using keywords |
| Search by filename | Searches through filenames where available |
| 2023-03-28 | Betacoronavirus | Blast database of Betacoronavirus nucleotide sequences. (Blast database full path and name - /fdb/blastdb/Betacoronavirus) |
| 2023-03-28 | NCBI nr Blast database | NCBI nonredundant comprehensive protein database, compiled from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF (Blast database full path and name - /fdb/blastdb/nr ) |
| 2023-03-28 | NCBI nt Blast database | NCBI nonredundant comprehensive nucleotide database, compiled from Genbank, Refseq, TPA and PDB. (Blast database full path and name - /fdb/blastdb/nt ) |
| 2023-03-28 | Patent nucleotide sequences Blast db | Patent nucleotide sequences (Blast database full path and name - /fdb/blastdb/patnt ) |
| 2023-03-28 | PDB protein sequences Blast db | Protein Data Bank sequences. (Blast database full path and name - /fdb/blastdb/pdbaa ) |
| 2023-03-28 | Swissprot Blast database | Curated, highly-annotated protein sequence database (Blast database full path and name - /fdb/blastdb/swissprot ) |
| 2023-03-28 | taxonomy | The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. |
| 2023-03-26 | UCSC goldenPath | The UCSC Genomics Institute maintains a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. |
| 2023-03-24 | I-TASSER ITLIB | I-TASSER Template Library for Protein Structure and Function Prediction |
| 2023-03-23 | UCSC gbdb | The UCSC Genomics Institute maintains a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. |
| 2023-03-21 | PDB nucleotide sequences Blast db | Protein Data Bank nucleotide sequences. (Blast database full path and name - /fdb/blastdb/pdbnt ) |
| 2023-02-22 | intogen | intogen is collecting data from TCGA, PCAWG, cBioPortal, Hartwig Medical Foundation, ICGC, St.Jude, PedcBioPortal, TARGET, Beat AML, and Literature. |
| 2023-02-22 | refdb | the data is collecting data from TCGA, PCAWG, cBioPortal, Hartwig Medical Foundation, ICGC, St.Jude, PedcBioPortal, TARGET, Beat AML, and Literature. |
| 2023-02-20 | EBI-GWAS | The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. |
| 2023-02-15 | VEP | VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. |
| 2023-02-10 | ensembl | Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. |
| 2023-01-30 | annovar | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. |
| 2023-01-19 | MSigDB | The Molecular Signatures Database (MSigDB) is a resource of tens of thousands of annotated gene sets for use with GSEA software, divided into Human and Mouse collections. Currently at version v2022.1 |
| 2022-10-17 | Standard databases for foldseek | foldseek provides prebuilt databases for AlphafoldDB (Swiss-Prot, Proteome, and UniProt50) as well as PDB. |
| 2022-10-16 | dfam | The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. |