Scientific Databases and Tools
Basic Tools for Research in Biochemistry
and Molecular Biology
- EMBL WWW Gateway
to Isoelectric Point Service
- Links
for siRNA and Hairpin Tools - Links to tools for short intefering RNA
(siRNA) and short hairpin RNA (shRNA) design using different algorithms. (Michael
McMannus, Massachusetts Institute of Technology)
- MIT Primer3 Input
- PCR primer design.
- Pedro's
BioMolecular Research Tools - A collection of tools and resources.
- Peptide Property
Calculator
- Protein Calculator
- Oligonucleotide
Properties Calculator
- Reverse Complement -
This utility "converts a DNA sequence into its reverse, complement, or reverse-complement
counterpart." (Pennsylvannia State University)
- RNAi Central - RNAi
resources, including siRNA and shRNA design tools. (Hannon Lab, Cold Spring
Harbor Laboratory)
- siDIRECT - Online
target-specific siRNA design program for mammalian RNA interference. (University
of Tokyo, Japan)
- 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)
Also see 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)
- The CMS Molecular Biology Resource
- Links to resources and tools in molecular biology, biotechnology, molecular
evolution, biochemistry and biomolecular modeling. (San Diego Supercomputer
Center)
- 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 EST Machine - Bioinformatics
resources for Expressed Sequence Tags analysis.
- 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)
- GenomeWeb - Collection
of links to genome-related sites. (Rosalind Franklin Centre for Genomics Research,
UK)
- 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)
- 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)
- National Center for Biotechnology
Information (NCBI) (National Library of Medicine, National Institutes
of Health)
- National Center for Genome Resources
- 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
- TBASE - "[A]n attempt to organize
information on transgenic animals and targeted mutations generated and analyzed
worldwide." (The Jackson Laboratory)
- 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).
- Whitehead Institute Center for Genome
Research - Information on map and sequence releases, software and people
at the Genome Center.
- WU BLAST - Washington University BLAST
archives. (Warren R. Gish, Washington University)
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
- 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.
- The CMS Molecular Biology Resource
- Links to resources and tools in molecular biology, biotechnology, molecular
evolution, biochemistry and biomolecular modeling. (San Diego Supercomputer
Center).
- 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)
- International Union of Biochemistry
and Molecular Biology (IUBMB)
- National Center for Biotechnology
Information (NCBI) (National Library of Medicine, National Institutes
of Health)
- 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
- Genetic Disorders and
Birth Defects
- 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
For an extensive collection of dictionaries, including scientific and medical,
see Open Directory:
Reference: Dictionaries.
- 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."
- Common Latin
Phrases and Abbreviations
- 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
Miscellaneous
Discussion Groups
See also the Discussion Groups section
of the General Biochemistry and Cell Biology page.