Bioinformatics Internet Resources Toolkit
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Select Databases
- BioMed Central - BioMed Central is an independent publishing house committed to providing immediate open access to peer-reviewed biomedical research. All original research articles published by BioMed Central are made freely and permanently accessible online immediately upon publication. Note that access to some content, such as reviews and paper reports, may be available only with a subscription.
Select BioMed Central Resources:
- Biology Image Library - The Biology Image Library is an online collection of images, movies, illustrations and animations across biology and biomedicine. All content is available to subscribers for non-commercial use; some images are also available for commercial use.
- Journals by Subject Area - Scroll down to see what is available for the subject category of interest, which may include Bioinformatics, Cancer, Genomics, Medical Genomics or one of the numerous other subject areas covered in this thematically- arranged index.
- Gateways - “Gateways” highlight the latest, most pertinent articles published in a given field. Some which may be of interest include:
Bioinformatics and Genomics, Cancer, Microarrays, Microbiology & Infectious Diseases, RNAi, Stem Cell and Systems Biology
- National Center for Biotechnology Information (NCBI) - NCBI provides access to biomedical and genomic information for use by researchers and the medical community via the creation of databases and tools for storing and analyzing knowledge about molecular biology, biochemistry, and genetics.
Selected NCBI Resources:
- BLAST - Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
- Cn3D - Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments which allows users to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D offers annotation and alignment editing features. This free, downloadable application runs on Windows, Macintosh, and Unix platforms.
- GenBank - GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Complete bimonthly releases and daily updates (incorporating international data) are available by FTP.
- Gene - Gene maintains information about genes from genomes of interest to the RefSeq group.
- Reference Sequence (RefSeq) - RefSeq is a curated collection of DNA, RNA, and protein sequences. It provides one example of each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes. For each model organism, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts.
- BRENDA: Comprehensive Enzyme Information System
BRENDA compiles comprehensive enzyme functional data from the primary literature and makes it available to the scientific community. It is available free of charge for researchers and non-profit organizations. - Broad Institute - Data produced and analytical software tools developed by The Broad Institute are openly shared with the entire scientific community. Data is arranged by organism/species, with links to relevant tools and project information; software tools allow for analysis of genome-related datasets.
- Entrez , The Life Sciences Search Engine - NCBI's retrieval system which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. Genome, Nucleotide, Protein and Structure are all available via the University Libraries Databases list.
- ExPASy (Expert Protein Analysis System) - Proteomics server of the Swiss Institute of Bioinformatics (SIB) dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. It is expected to be renamed as SIB Bioinformatics Resource Portal in Spring 2011 and upgraded to include access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. This new portal is presently available as ExPASy-beta.
- GOLD (Genomes Online Database) - An online resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.
- Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff - HGMD represents an attempt to collate known (published) gene lesions responsible for human inherited disease. The public version of this database is freely available to users from academic institutions and non-profit organizations. Free registration is required.
- J. Craig Venter Institute - Links to various software, mathematical tools, and databases to assemble and analyze genomic data.
- NCI Center for Bioinformatics - Provides links to numerous tools and resources to promote information sharing. NCICB offers open-source infrastructure components that others can use to develop databases and software tools to meet specific research needs.
- OBRC: Online Bioinformatics Resources Collection - This collection from the University of Pittsburgh Health Sciences Library System provides several tools for finding information on genes and proteins, metabolic and signaling pathways, and experimental protocols.
- PharmGKB - The Pharmacogenomics Knowledge Base focuses on collecting, encoding, and disseminating knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.
- RCSB Protein Data Bank - RCSB Protein Data Bank is an archive containing information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Provides a variety of tools and resources allowing users to perform searches based on annotations relating to sequence, structure and function. All data is curated and annotated according to wwPDB standards.
Organism-Specific Databases