Scientific Databases

A set of centrally-maintained and updated scientific databases is made available to users of Helix and Biowulf. Click on a link below to see the available databases. [List of genomes]

Blast	formatted for the NCBI Blast program. For use via command-line Blast on HPC systems.
Fasta	Fasta-format flatfile databases used by Fasta, Blat and other programs.
MySQL	Accessible through the HPC mirror of the UCSC Genome Browser. Also available for direct MySQL queries from the Biowulf cluster nodes.
PDB	Protein Data Bank 3-D structures of macromolecules. Can be accessed at /pdb on any HPC system, or users can samba-mount the PDB database on their own systems.
CSD	Cambridge Structural Database. Can be accessed through WebCSD (NIH access only)
PFAM	A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Used by HMMER and other programs.
VCF	Variant Call Format for genomic data
BAM	Binary SAM files
.fai	Fasta index file produced by samtools faidx
.dict	Sequence dictionary file produced by Picard CreateSequenceDictionary
Annotations	Genome annotations
Igenomes	Illumina's Igenomes are a collection of reference sequences and annotation files for commonly analyzed organisms. More info at Illumina
Hisat indexes	Indexes for the Hisat program for mapping RNA-seq reads
Hiseq data	For Illumina HiSeq Analysis
Defuse data	Data used by the deFuse program for gene fusion discovery using RNA-Seq data
Plinkseq data	Data used by plinkseq, a library for working with human genetic variation data.
Novoalign indexes	Indexes for the Novoalign aligner for single-ended and paired-end reads from the Illumina Genome Analyser
Fusionmap indexes	Used by the fusionmap program for fusion alignment
Gemini data	For use by the Gemini program to explore genomic variation
DSSP	A database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
Bfast indexes	For use by the Bfast program for fast and accurate mapping of short reads to reference sequences
GENCODE	The GENCODE Project: Encyclopaedia of genes and gene variants.
HMMER indices	Indexed for the HMMER program that uses profile hidden Markov models for biological sequence analysis
Impute2	Reference data for the Impute program for genotype imputation and haplotype phasing
picrust	Data for the picrust program which represents Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST).
APT	Files for Affymetrix GeneChipR arrays
gimmemotifs	index files for gimmemotifs
hapmap	files used for hapmap to identify and catalog genetic similarities and differences in human beings
homer	files used for homer that is for Motif Discovery and ChIP-Seq analysis
igenomes_extra	files related to igenomes but are not directly downloaded from the formal release of illumina igenomes.
miso	indexes used for miso which is used for quantitates the expression level of alternatively spliced genes from RNA-Seq data.
rseg	Rseg chromosome size file
sratoolkit	files for sratoolkit
plinkseq	Genome files used by plinkseq program.
gmap/gsnap indices	indices used for alignments with gmap/gsnap
GATK resource bundle	Standard data set for working with GATK
dbNSFP	dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. The data is in a tab-delimited file with header descriptions.
minimac	1000 genomes data for minimac genotype imputation
kraken	Databases for the kraken taxonomic classification system
VEP data	For use by the VEP program.
Meme	Meme databases
ANNOVAR	Tab-delimited text files for use with ANNOVAR.
taxonomy	NCBI Taxonomy database dump files
Mascot	For use by the Mascot search engine

Genomes