Scientific Reference Data

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.


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Browse Common Databases

Recently Updated:

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.