Scientific Databases and Tools
Basic Tools
- EMBL WWW Gateway to Isoelectric Point Service
- JustBio Hosted Tools - A range of online tools for DNA, RNA and protein work (requires free registration).
- Molecular Toolkit - Utilities to analyze and manipulate nucleic acid and protein sequences. (R.A. Bowen, Colorado State University)
- Molecular Station - A portal for molecular biology, DNA, RNA and protein work, proteomics, protocols, bioinformatics and product information.
- Peptide Properties Calculator - Calculate hydropathy plots, extinction coefficients and approximate volumes of proteins.
- SimGene.com - Molecular biology and bioinformatics tools.
- PCR Station - Polymerase chain reaction (PCR) resources.
- Real Time PCR Primer Sets - Validated primer sets for quantitative real-time PCR.
- NEBCutter - "This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once."
- Rebase - Restriction enzyme database.
- RestrictionMapper - Find restriction sites in DNA sequence.
- Webcutter - Find restriction sites in DNA sequence.
- The MIT/ICBP siRNA Database - "The MIT [Massachusetts Institute of Technology]/ICBP [Integrative Cancer Biology Program] siRNA Database is a university-wide effort to catalog these experimentally validated reagents and make that information available to other researchers, both within and outside the MIT community." (Massachusetts Institute of Technology)
- RNAi Central - RNAi resources, including siRNA and shRNA design tools. (Hannon Lab, Cold Spring Harbor Laboratory)
- The RNAi Web - General resource.
- siDIRECT - Online target-specific siRNA design program for mammalian RNA interference. (University of Tokyo, Japan)
- siRNA Database - [A] comprehensive siRNA database that contains siRNA targets against all known mRNA sequences throughout a variety of organisms.." (Part of the Protein Lounge systems biology Web site)
- siRNA Database and Resources for RNA Interference Studies
- siRNA Selector - "A set of rules was used for evaluating siRNA functionality based on thermodynamics parameters (Khvorova et al., 2003, Schwarz et al., 2003) and sequence-related determinants developed by Dharmacon (Reynolds et al., 2004). Specificity is determined using BLAST against UniGene databases." (Wistar Institute)
- siRNA Target Finder (Ambion)
- The Engineering Tool Box
- Radioactive Decay Calculator (Environmental Health and Safety, University of Washington)
See also the Methods, Protocols and Techniques page.
General Nucleic Acid, Gene and Genomics Databases
- Alphabetical List of Knockout Genes - Genes that have been knocked out in the mouse.
- BodyMap - An anatomical expression database of human genes.
- CBS Prediction Servers - Nucleotide and amino acid sequence-based bioinformatics tools for structure and function prediction. (Center for Biological Sequence Analysis, Technical University of Denmark DTU)
- CMS Molecular Biology Resource - Links to resources and tools in molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
- EBI Services - Access to nucleic acid, protein and macromolecular structure databases, including the EMBL-Bank database. (European Molecular Biology Laboratory - European Bioinformatics Institute)
- BLAST @ EBI - Perform BLAST (Basic Local Alignment Search Tool) searches.
- ClustalW - "[A] general purpose multiple sequence alignment program for DNA or proteins."
- FASTA - "Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs.
- The European Ribosomal RNA Database - Ribosomal RNA (rRNA) sequence data listed by organism, secondary structure prediction programs and other software, links to related sites. (Peter De Rijk, University of Antwerp, Belgium)
- Genomes OnLine Database - "GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. GOLD provides the largest available and most detailed monitoring of genome sequencing projects." (Nikos Kyrpides, Lawrence Berkeley National Laboratory)
- GOBASE - The Organelle Genome Database - "GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. In its next phase, GOBASE will also include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts." (Université de Montréal, Canada)
- HUGO Gene Nomenclature Committee (HGNC) - "For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database." (US National Human Genome Research Institute and the Wellcome Trust, UK)
- Human Genome Project Information - Links to Human Genome Project sites and other genomic research sites.
- Induced Mutant Resource - List of transgenic and targeted mutant mice. (Jackson Laboratory)
- International Union of Biochemistry and Molecular Biology (IUBMB)
- IUBMB Nomenclature
- Nucleic Acids
- Knockout Mouse Station
- Microarray Station
- National Center for Biotechnology Information (NCBI) (National Library of Medicine, National Institutes of Health)
- BLAST Search
- Entrez - Database search and retrieval system.
- Cancer Chromosomes
- Gene
- Genome
- Genome Project - "The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms."
- GEO - Gene Expression Omnibus
- GEO Data Sets
- HomoloGene
- Nucleotide
- Online Mendelian Inheritance in Man (OMIM)
- PopSet (population study data sets)
- Single Nucleotide Polymorphism (SNP)
- Taxonomy
- UniGene
- Genomic Biology - "NCBI provides several genomic biology tools and resources, including organism-specific pages that include links to many web sites and databases relevant to that species."
- Chicken Genome Resources
-
Dictyostelium Genome Resources
- Dog Genome Resources
-
Drosophila Genome Resources
- Human Genome Resources
- Mouse Genome Resources
- Plant Genomes
- Rat Genome Resources
- Sea Urchin Genome Resources
-
Xenopus Genome Resources
- Zebrafish Genome Resources
- Open Reading Frame (ORF) Finder
- Serial Analysis of Gene Expression (SAGE)
- Submit to Genbank
- National Center for Genome Resources
- MicroarracyWorld - Resources for microarrays and expression profiling.
- MicrobesOnline - Browse and compare prokaryotic genomes. (Lawrence Berkeley National Laboratory)
- Public Microarray Databases - Links to gene expression and microarray databases.
- Stanford Genomic Resources
- The Arabidopsis Information Resource (TAIR) - A "comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant." (Carnegie Institution of Washington, Stanford University and the National Center for Genome Resources)
-
Candida Genome Database - A "resource for genomic sequence data and gene and protein information for Candida albicans."
- PharmGKB - An "integrated resource about how variation in human gene leads to variation in our response to drug."
-
Sacchoromyces Genome Database (SGD) - "SGD is an organized collection of genetic and molecular biological information about Saccharomyces cerevisiae, bakers' and brewers' yeast. It contains the sequences of yeast genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; links to literature information; links to functional genomics datasets; and tools for analysis and comparison of sequences."
- SOURCE - A "unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports."
- Stanford Microarray Database (SMD) - "SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data are released to the public at the researcher's discretion or upon publication."
-
Tetrahymena Genome Database - A "web-accessible database for the Tetrahymena genomic sequence information" with "information on the genome, genes and proteins of Tetrahymena collected from the scientific literature, research community and many other sources."
- Table of Standard Genetic Code
- Transcription Regulatory Regions Database - Links to gene databases and information on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, such as transcription factor binding sites, promoters, enhancers and silencers, and expression patterns of the genes. (Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences)
- WU BLAST - Washington University BLAST archives. (Warren R. Gish, Washington University)
- WWW Virtual Library of Genetics
- WWW Virtual Library of Model Organisms
For more species-specific genome and other databases, see the Model Organisms section of the Molecular and Cell Biology of Development page.
General Protein and Proteomics Databases
- Antibody & Beyond - Tool for finding antibodies, basic information on antibodies, techniques and applications.
- The Antibody Resource Page - The name says it all.
- CBS Prediction Servers (Center for Biological Sequence Analysis, Technical University of Denmark DTU) - Nucleotide and amino acid sequence-based bioinformatics tools for structure and function prediction.
- CMS Molecular Biology Resource - Links to resources and tools in molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
- EBI Services - Access to nucleic acid, protein and macromolecular structure databases, including the EMBL-Bank database. (European Molecular Biology Laboratory - European Bioinformatics Institute)
- BLAST @ EBI - Perform BLAST (Basic Local Alignment Search Tool) searches.
- ClustalW - "[A] general purpose multiple sequence alignment program for DNA or proteins."
- FASTA - "Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs."
- InterProScan
- ExPASy Proteomics Server - Search protein databases such as SWISS-PROT, Trembl, PROSITE, ENZYME, etc. (Swiss Institute of Bioinformatics)
- ExPASy Proteomics Tools - Proteomics and sequence analysis tools.
- ExPASy Biochemical Pathways - "This page gives access to the digitized version of the Roche Applied Science 'Biochemical Pathways' wall chart."
- iHOP - Information Hyperlinked over Proteins - "By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research." (Robert Hoffmann)
- International Union of Biochemistry and Molecular Biology (IUBMB)
- Amino Acids and Peptides
- IUBMB Nomenclature
- MPR: Mammalian Phosphorylation Resource - An expert-curated resource that provides sequence-based integration of information on antibodies against phosphorylation sites on human proteins.
- National Center for Biotechnology Information (NCBI) (National Library of Medicine, National Institutes of Health)
- BLAST Search
- Entrez - Database search and retrieval system.
- Conserved Domains
- Protein
- Peptide Station - Links to resources devoted to peptides, peptide-related protocols and peptide synthesis.
- UniProt (Universal Protein Resource) - Catalog of sequence and function information on proteins from Swiss-Prot, TrEMBL and PIR.
- WU BLAST - Washington University BLAST archives. (Warren R. Gish, Washington University)
See also the the Macromolecular Structure Databases section of the Structural Biology page for protein structure databases (PDB, etc.) and the Protein Classes and Families section of the Proteins: Biogenesis to Degradation page for databases on specific protein families.
(Collections of Enzyme Functional and Nomenclature Data)
(Data Collections on Metabolic Pathways)
(Data Collections on Regulatory Pathways)
Other Biological Databases
- NeuroMouse - "[I]nformation on distribution of the current version of NeuroMouse, an interactive ToolBook-based, object-oriented database of murine neurologic information. This system provides an integrated resource for the characterization and description of mammalian neurologic data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas." (Jeffrey Henderson, University of Toronto)
- neuronetbase.org - A database of "electrophysiological and other information describing cortical neurons and their characteristic responses to somatosensory and other stimuli." (Daniel Gardner, Cornell University Medical Center)
Statistical Information
- Error Analysis in Experimental Physical Science
- GraphPad Library - Articles, books, manuals and links on data analysis, curve fitting and biostatistics. (GraphPad Software)
- Q-Test
- Statistics: Propogation of Errors
- The Ubiquitous Sample Mean
English Language References
- Common Errors in English (Paul Brians, Professor of English, Washington State University)
- List of Errors
- Non-Errors - "Those usages people keep telling you are wrong but which are actually standard in English.
- Dictionary.com
- The King's English (Fowler, H.W., 1908)
- The Mayfield Handbook of Technical and Scientific Writing
- Medical Abbreviations Dictionary (MediLexicon) - " A dictionary of over 200,000 medical, pharmaceutical, biomedical & healthcare acronyms and abbreviations. Plus medical news and searches for the medical, pharmaceutical or healthcare professional." (Pharma-Lexicon International)
- Merriam-Webster Online
- The Elements of Style (Strunk, William, Jr., 1918)
- Thesaurus.com
For an extensive collection of dictionaries, including scientific and medical, see Open Directory: Reference: Dictionaries.
Miscellaneous
- HTML 4.0 Entities for Symbols and Greek Letters
- Magical Macintosh Key Sequences
- metric conversions.org - Online conversion calculators, tables and metric formulas.
- Online Conversion
- Quintessential Vita Sample
- United States Postal Service Postage Rate Calculator
- World Database of Happiness
Discussion Groups
- Usenet newsgroup archives from BIOSCI/bionet (can also be accessed through Google Groups: bionet):
- ARRAYS/bionet.molbio.genearrays - Gene array and microarray technology.
- AUTOSEQ/bionet.genome.autosequencing - Research and support on automated DNA sequencing.
- BIOCHROM/bionet.genome.chromosomes - Mapping and sequencing of eukaryotic chromosomes.
- BIO-MATRIX/bionet.molbio.bio-matrix - Computer applications to biological databases.
- BIO-WWW/bionet.software.www - Information about WWW sources of interest to biologists.
- EMBL-DB/bionet.molbio.embldatabank - Information about the EMBL nucleic acid database.
- GENBANKB/bionet.molbio.genbank - Information about the GenBank nucleic acid database.
- GNOMEPR/bionet.molbio.genome-program - Discussions regarding the international Human Genome Project.
- MOLREPS/bionet.molecules.repertoires - Generation and use of libraries of molecules.
See also the Discussion Groups section of the General Resources and Tutorials page.
@ 1999-2017 Gabriel Fenteany 
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