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 |
| 2025-11-05 | ensembl | Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. |
| 2025-09-20 | Betacoronavirus | Blast database of Betacoronavirus nucleotide sequences. (Blast database full path and name - /fdb/blastdb/Betacoronavirus) |
| 2025-09-20 | 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 ) |
| 2025-09-20 | 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 ) |
| 2025-09-20 | Patent nucleotide sequences Blast db | Patent nucleotide sequences (Blast database full path and name - /fdb/blastdb/patnt ) |
| 2025-09-20 | PDB protein sequences Blast db | Protein Data Bank sequences. (Blast database full path and name - /fdb/blastdb/pdbaa ) |
| 2025-09-20 | Swissprot Blast database | Curated, highly-annotated protein sequence database (Blast database full path and name - /fdb/blastdb/swissprot ) |
| 2025-09-20 | taxonomy | The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. |
| 2025-09-15 | NCBI SRA Refseq data | NCBI SRA Refseq data |
| 2025-09-14 | Protein Data Bank | An archive of experimentally determined three-dimensional structures of biological macromolecules. |
| 2025-09-12 | antismash | PFAM and ClusterBlast databases for antiSMASH |
| 2025-09-10 | Oxford Nanopore Technologies Benchmark Datasets | The ont-open-data registry provides reference sequencing data from Oxford Nanopore Technologies to support, 1) Exploration of the characteristics of nanopore sequence data. 2) Assessment and reproduction of performance benchmarks 3) Development of tools and methods. The data deposited showcases DNA sequences from a representative subset of sequencing chemistries. The datasets correspond to publicly-available reference samples (e.g. Genome In A Bottle reference cell lines). Raw data are provided with metadata and scripts to describe sample and data provenance. |
| 2025-09-06 | PDB nucleotide sequences Blast db | Protein Data Bank nucleotide sequences. (Blast database full path and name - /fdb/blastdb/pdbnt ) |
| 2025-08-14 | Human Pangenome HPRC Assemblies Release 2 | Assembly data from the Human Pangenome Reference Consortium, release version 2 |
| 2025-07-31 | RepBase | Repbase is the most commonly used database of repetitive DNA elements. |
| 2025-06-29 | 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. |
| 2025-06-24 | GENCODE | The goal of the GENCODE project is to identify and classify all gene features in the human and mouse genomes with high accuracy based on biological evidence, and to release these annotations for the benefit of biomedical research and genome interpretation. |
| 2025-06-24 | 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. |
| 2025-05-09 | annovar | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. |
| 2025-04-29 | diamond databases | Select reference databases for the diamond application |