Scientific Databases and Tools
Basic Tools
- 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)
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)
- Knockout Mouse Station
- Microarray Station
- National Center for Biotechnology
Information (NCBI) (National Library of Medicine, National Institutes
of Health)
- 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)
- 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)
- 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)
- 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
English Language References
- Common Errors in
English (Paul Brians, Professor of English, Washington State University)
- 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
Discussion Groups
See also the Discussion
Groups section of the General
Resources and Tutorials page.
