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Bioinformatics

Data Science Specialist

Jeffrey Oliver's picture
Jeffrey Oliver
Contact:
Office of Digital Innovation & Stewardship
University Libraries
University of Arizona
Tucson, AZ 85721
520-626-9215

NCBI databases & tools

The National Center for Biotechnology Information (NCBI) hosts several bioinformatic databases as well as analytical resources. These are but a few of the more popular databases; for a full listing, explore the NCBI site. There is also a YouTube channel with a variety of training materials for using NCBI resources.

1000 Genomes The 1000 Genomes Browser is an interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project.
NCBI BLAST BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
NCBI ClinVar ClinVar is a public, tracked record of reported relationships between human genetic variation and observed health status with supporting evidence. All records Include a review status of the evidence for given clinical assertions and links to original research.
E-Utilities The E-utilities API provides programmatic access to several NCBI databases, including PubMed, Genome, Nucleotide, and dbSNP. EDirect offers UNIX command-line utilities for automating E-Utilities queries and processing results.
NCBI Gene Database Gene contains curated information about genes from a variety of species. Records include nomenclature, chromosomal location, gene products, phenotypes, and links to citations and external databases.
Gene Expression Omnibus The Gene Expression Omnibus is a public functional genomics data repository of curated gene expression profiles. The related tool, GEO2R, can be used to perform differential expression analyses on GEO Series
Genetic Testing Registry The Genetic Testing Registry houses information on genetic tests and laboratories, including single-gene tests as well as arrays, panels, and pharmacogenetic tests.
NCBI MedGen MedGen organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. You can use the database to search for relationships between medical conditions and specific genes.
NCBI Nucleotide Database The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
NCBI SRA Database The Sequence Read Archive is NIH's primary archive of high-throughput sequencing data from a variety of sequencing platforms, including Roche 454, Illumina, ABI, and PacBio.