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Bioinformatics@HSL: Databases

Selected Bioinformatics Databases

NCBI: National Center for Biotechnology Information
The NCBI has a large number of interlinked specialty databases useful to molecular biologists, geneticists, and others researching genetic and protein sequences.  The "How To" section of the NCBI site provides strategies for obtaining specific data from the system.
Ensembl Genome Browser
Ensembl is a software system which produces and maintains automatic annotation on selected eukaryotic genomes and is jointly developed by EMBL - EBI and the Wellcome Trust Sanger Institute. (Source: provider website)
UCSC Genome Browser
This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects. UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC). (Source: provider website)
SIB ExPASy Bioinformactice Resource Portal
Integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences: proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

Local UNC Software

 
The UNC Center for Bioinformatics supports many common bioinformatics software packages that are licensed for use by UNC personnel. Current software resources include:
 
Vector NTI                                           GCG
CLC Genomics Workbench               Sequencher
GeneSpring                                          Partek
IPA
 
For more information on these resources, see the UNC Center for Bioinformatics software page.

Bioinformatics Resource Discovery Tools

Nucleic Acids Research Annual Database Issue
Nucleic Acids Research annually collates, indexes, and summarizes new or revised databases available for research in molecular biology, genetics, genomics, and proteomics. The 2014 database issue is freely accessible and includes descriptions of 58 new and 123 updated data resources. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. The companion online Database Collection, organized by category at http://www.oxfordjournals.org/nar/database/c/, now includes over 1550 selected databases spanning various aspects of molecular and cell biology.  (Source: NAR website)
Nucleic Acids Research Annual Web Server Issue
NAR issue dedicated to web-based software resources for analysis and visualization of molecular biology data. It is freely available under NAR's open access policy. The 2013 issue reports on 95 web servers with special emphasis on network and pathway analysis, high-throughput sequencing data analysis and biological text mining.  (Source: NAR website)
Bioinformatics Links Directory
This freely accessible, online collection features curated links to molecular biology resources, tools and databases.  Links listed in this collection are selected based on recommendations from bioinformatics experts in the field and input from the community of bioinformatics users. Since 2003 it lists all links contained in the annual NAR Web Server Issue. (Source: bioinformatics.ca website)
 
OBRC: Online Bioinformatics Resources Collection (University of Pittsburgh Health Sciences Library System)
The Online Bioinformatics Resources Collection (OBRC) contains annotations and links for 2826 (and growing) 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.

Literature Databases