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Bioinformatics Databases |
This Focus On guide is designed to help researchers identify and access the major databases for bioinformatics research,
including sequencing, structure, and analysis tools as well as literature databases and tools for discovering new resources
for genetic, genomic, and proteomic data analysis. Please feel free to use our
use our Ask a Librarian
service for additional assistance in identifying appropriate resources
for your work (note: this and all other links on this page will open a
new browser window).
- Entrez cross-database search
- This portal provides access to all of the National Institutes of
Health - National Center for Biotechnology Information databases,
including PubMed, OMIM, "Nucleotides" (RefSeq and GenBank), "Proteins"
(PDB, PIR), and dbSNP. There are more than 30 databases available via
this metasearch-enabled entry point. To ensure you have access to
UNC-subscribed electronic journals, first access PubMed
via a UNC-sponsored link, then click the words "All Databases " in the
black navigation bar at the top of the screen. A description of each database is available from the Health Sciences Library
here.
- Vector NTI Advance 10
- The modules that make up the Vector NTI system support annotation, assembly, blast searching, translation, primer design, in silico cloning, and a number of other common tools. The graphical interface, image quality, and ease of information import and export from the Vector NTI system are very user friendly. Vector NTI Advance includes the following programs: Vector NTI, Align X, ContigExpress, GenomBench, Bioannotator, and Explorer Database. This software is available only from Invitrogen who provides a static license to any academic/non-profit user. Individuals may install on three workstations and are responsible for renewing the license every year with Invitrogen. Additional software tools and resources can be found on the UNC-Chapel Hill Center for Bioinformatics website.
- GeneSpring
- GeneSpring (Agilent Technologies, Palo Alto, CA), microarray data analysis software, provides a convenient means to statistically analyze microarray data of both one-color and two-color experiments. The user-friendly designed GUI of GeneSpring allows users to graphically monitor analysis procedure and display results. GeneSpring also allows users to update genome information from GenBank, UniGene and LocusLink, annotate genes of interest based on the simplified Gene Ontology Annotations, map genes to biochemical pathways and to cytogenetic bands on chromosomes, and even generate gene homology tables cross species. This software is available to UNC-Chapel Hill researchers through a site license. Additional software tools and resources can be found on the UNC-Chapel Hill Center for Bioinformatics website.
- Sequencher
- A program for DNA sequence analysis, including contig assembly. This software is available to UNC-Chapel Hill researchers through a site license. This and additional software tools and resources can be found on the UNC-Chapel Hill Center for Bioinformatics website.
- ExPASy Proteomics Server
- "The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB)
is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE." Databases include Swiss-Prot,
TrEMBL, and their derivatives. This mirror site is located at
the NC Supercomputing Center in the RTP and should be the fastest for use by UNC researchers.
- PubMed
- PubMed, a service of the National Library of Medicine, includes
over 14 million citations for biomedical articles back to the 1950's.
These citations are from MEDLINE and additional life science journals.
PubMed includes links to many sites providing full text articles and
other related resources.
- BIOSIS Previews
- BIOSIS Previews is a comprehensive biological sciences product
that is available via the ISI Web of Science® platform. Updated weekly,
it combines the content from Biological Abstracts® and Biological
Abstracts/RRM® (Reports, Reviews, Meetings) with the speed,
flexibility, and easy navigation of the ISI Web of Science. BIOSIS
Previews provides approximately 13 million records from nearly 5,000
life sciences journals and non-journal literature, including
conferences, meetings, symposia, review articles, U.S. patents, books,
book chapters, and software reviews. (Source: vendor website)
For access to other subject-specific article databases, please browse or search UNC's E-Research Tools system. Good subject categories for finding literature databases relevant to
bioinformatics research include Biology, Genetics, Information & Library Science, and Medicine.
- Nucleic Acids Research Molecular Biology Database Collection
- Every January the journal Nucleic Acids Research collates, indexes,
and summarizes new or revised databases available for research in
molecular biology, genetics, genomics, and proteomics. The total list
of databases is free and online in the MBDC.
- University of British Columbia Bioinformatics Centre: Links Directory
- This directory includes a number of databases and other web
resources, divided into eight topical areas: computer related, DNA,
education, expression, human genome, literature, model organisms, other molecules, protein, RNA, and sequence comparison.
- University of Washington HealthLinks Toolkits
- The Bioresearcher
section of this multi-level biomedical resources "toolkit" is of
particular use to bioinformatics researchers and educators. Included
are databases, news and community resources, and other websites of
interest to scientists working with biomolecules, cells & tissues,
organisms & populations, computer & laboratory systems, and
education & training programs.
- University of Pittsburgh Health Sciences Library System OBRC: Online Bioinformatics Resources Collection
- The Online Bioinformatics Resources Collection (OBRC) contains annotations and links over 1700 bioinformatics databases and software tools on the web. Included are databases and web-based tools in thirteen topical categories: DNA sequence databases and analysis tools; enzymes and pathways; gene mutations, genetic variations and diseases; genomics databases and analysis tools; immunological databases and tools; microarray, SAGE, and other gene expression; organelle databases; other databases and tools (literature mining, lab protocols, medical topics, and others); plant databases; protein sequence databases and analytical tools; proteomics resources; RNA databases and analysis tools; structure databases and analysis tools. The OBRC uses the Vivisimo Clustering Engine® to enhance retrieval and navigation of search results.
- Focus on Clinical Genetics and Genomics
- This guide includes databases and other online resources (including
journals and e-books) for clinicians and patients needing information
about genetically-linked diseases. Databases for cancer, mental
illness, and rare diseases/orphan drugs are highlighted along with more
general databases such as GeneTests and OMIM.
- Focus on Pharmacogenomics and Pharmacogenetics
- This short guide highlights drug discovery and development databases and other resources for pharmacogenomics.
Getting Help
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More resources for the bioinformatics community are available at Bioinformatics@HSL
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