Molecular Biology & Genetics

Bioscience: - Comprehensive Sites and Link Lists

• Amos' WWW links page - The ExPASy list of Biomolecular servers.
• Biology Links - From the Department of Cellular and Molecular Biology (Harvard University).
• BioToolKit- an annotated database of over 1129 online resources of interest to molecular biologists.
• Cell & Molecular Biology online - An informational resource for cell and molecular biologists.
• CMS Molecular Biology Resources- A compendium of electronic and Internet-accessible tools and resources for molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.
• Research Tools- In cell & gene collections, nucleic acid & protein databases, model organisms genomes, compound databases, literature and others sources.
• Highveld.com - The Internet Directory of Molecular Biology and Biotechnology.
  Laboratory Protocols, The Polymerase Chain Reaction, Molecular Biology Journals, Molecular Microbiology, Molecular Genetics, Molecular Biology Jumpstations, Companies and Suppliers, Genomes and Databases, Newsgroups and Mail Lists, Probiotics, Ribozymes, Peptide Nucleic Acid (PNA), NMR for the Molecular Biologist, Functional Genomics, Molecular Biology Books
• JustBio - BioInformatics and services for molecular biology scientists.
• MolBiol and Genetics - Links from the Max-Planck-Institute of Molecular Genetics for centers & institutes, information & literature databases, sequence databases & analysis, mapping, journals, carreers and much more.
• WWW Virtual Library - With directories for Bioscience, Biotechnology and more.

Genomics

• Nature's Genome Gateway
• Ensemble Genome Server - annotation on eukaryotic genomes.
• National Center for Biotechnology Information (NCBI) - Creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
  • The Site Map page explains all the NCBI resources.
  • Entrez - provides integrated access to nucleotide and protein sequence data.
  • Molecular Databases - For sequences, structures and taxonomy.
  • Genomic Biology - Provides resources for the human genome and other genomes
  • Data Mining Tools.
• TIGR Gene Indices
• UCSC Genome Bioinformatics
• euGenes - Genomic Information for Eukaryotic Organisms

• NCBI's Human Genome Resources
• OMIM - Online Mendelian Inheritance in Man
• UK Human Genome Mapping Project Resource Center - GenomeWeb etc.
• GeneCards- Human genes, map, proteins and diseases.
• The Genome Database (Site Map)
• Human Genome Variation Society including Variation Databases and Related Sites
• Human Gene Mutation Database including Locus-Specific Mutation databases
• Tumor Gene Database

• NCBI's Model Organism Guide
• Internet Resources to Biological Model Organisms - From the virtual library.

• Yeast Resource Center
• The Gietz Lab Yeast Transformation Home Page
• S. pombe Genome Project

• Mouse Genome Informatics at the Jackson Laboratory
• Mouse Genome Resources at NCBI
• Pathbase — A database of normal and transgenic mouse histology.
• Mouse Brain Library
• European Mouse Mutant Archive

• C. elegans resources at NCBI
• Caenorhabditis elegans WWW server
• WormBase
• Worm Atlas
• Blaxter Lab Nematode Genomics
• C. elegans Genome Project at the Sanger Sequencing Center
• Caenorhabditis Genetics Center
• Worm-Labs

• Drosophila melanogaster resources at NCBI.
• FlyBase
• The interactive Fly
• The Berkeley Drosophila Genome Project
• Drosophila at the Virtual Library.

• Rattus norvegicus resources at NCBI
• Recommended reading:

  Howard J. Jacob and Anne E.Kwitek (2002).
  Rat Genetics: Attaching Physiology and Pharmacology to the Genome
  Nature Reviews/Genetic1:33-42

• Zebrafish resources at NCBI.
• Zebrafish Information Network
• WashingtonU Zebrafish Genome Resources Project
• Danio rerio Sequencing Project
• Zebrafish WebServer (Massachusetts General Hospital)

Organelles Genetic Resources

• Organelles resources at NCBI.

Plant Genetic Resources

• Arabidopsis Resources
• Arabidopsis Information Resource
• Plant Genomes Central- The plant genome resources at NCBI.

Proteomics

• ExPASy - the Expert Protein Analysis System, a Proteomics and Molecular Biology Server for the analysis of protein sequences and structures as well as 2-D PAGE. A well organized collection of < 100 web links.
  • The Site Map page explains all the ExPASy resources
  Main resources are:
  • SWISS-PROT and TrEMBL- The annotated protein sequence database with cross references to many databases plus a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT.
  • Proteomic Tools is a great site with many links for protein analysis including Protein identification and characterization, DNA - Protein translation, similarity searches, pattern and profile searches, post-translational modification prediction, primary structure analysis, secondary structure prediction, tertiary structure, transmembrane regions detection or sequence alignment.
  • 2D-Gel-Electrophoresis Resources includes data on proteins identified on various 2-D PAGE reference maps and links to 2D-databases, services and software, journals and meetings. Related databases are:
    • WORLD-2DPAGE - A collection of 2D-Databases of many organisms or
    • 2D-HUNT - The 2D Electrophoresis Finder.
  • Human Proteomics Initiative

• Protein Information Resources

• NCI 2DWG Image Meta-Database
• 2D- Electrophoresis Tutorial

• BSM - The Biomolecular Structure and Modelling Group.
• Predict Protein Structures
• BioMagResBank- A database of NMR-derived protein structures from BIMAS-NIH.
• Enzyme Structures Database
• European Bioinformatics Institute - A center for research and services in bioinformatics.
• InterPro - For whole genome analysis.
• Proteome Databases 
• Database of Interacting Proteins

Research Toolbox

Bench-Protocols

• Molecular Biology On-Line Resources - With general research tools, protocols, supplies, equipment, journals, a forum for discussion on methods etc.
• Protocols for recombinant DNA isolation, cloning, and sequenzing.
• Nucleic Acids Research Methods Online.

Specialized Resources

• User Guide to HPLC

• Base Peak - A general mass spectrometry resource.
• UCSF Mass Spectrometry Facility

• Large-Scale Gene Expression and Microarray Links and Resources
• DNA Microarray (Genome Chip)
• UCSD Array Science - Includes HAPI, the High-density Array Pattern Interpreter.
• and don't forget to look up the WWW Virtual Library or the Comprehensive Sites

• Laboratory for Optical and Computational Instrumentation
• Microscopy and Imaging Resources on the WWW

Sequence Analysis Tools

• The Sequence Manipulation Suite
• Technical Literature on-line - From New England Bioloabs
• Cloning Vectors from BD Biosciences (Clonetech)
• Restriction Enzyme Database
• Restrictionmapper
• WebCutter
• The Primer Generator
• Primer3
• Calculate the thermal denaturation profile - of double stranded RNA or DNA.

• Comparative RNA Web Site
• RNABase
• RNA Modification Database - From the Departments of Medicinal Chemistry and Biochemistry, Univ. of Utah.
• RNA World - From the Institute of molecular biotechnology (Jena, Germany).
• RNAi Technical Resources and RNA Structure/Function Tools - from Ambion - The RNA Company

• The Tree of Life- A phylogenetic navigation system for the internet.
• Phylogenetic Resources - From UCMP.
• Phylogeny and Reconstructing phylogenetic trees
• "Deep Green" - The green plant phylogeny home page.
• Software products for phylogenetic analysis are found at Taxonomy, Systematics, and Bioinformatics at the University of Glasgow

Equipment and Supplies

• Biocompare - The buyer's guide for life scientists.
• BioSupplyNet - A great site to find what you need for labwork.

Software

• Biocatalog - A software directory of general interest in molecular biology and genetics.
• Genamics - Software development.
• Genetics Computer Group (GCG)- Solutions for nucleic acids and protein analysis.
• and don't forget to look up the Biotechnology Information Library of the WWW Virtual Library or the Comprehensive Sites

Databases, Pathways and more

• The January volumes of Nucleic Acid Research. Starting in 1994, NAR dedicates a volume annualy to scientific databases. Included is a collection of over 700 Molecular Biology Databases devided into the following categories:
  - Nucleotide Sequence Databases, RNA sequence databases, Protein sequence databases, Structure Databases, Genomics Databases (non-vertebrate), Metabolic and Signaling Pathways, Human and other Vertebrate Genomes, Human Genes and Diseases, Microarray Data and other Gene Expression Databases, Proteomics Resources, Other Molecular Biology Databases, Organelle databases, Plant databases, Immunological databases.
  The latest volume is:
  • Nucleic Acids Research (2005) Database Issue
• DBCat - The public catalog of databases.
• Pathways - BioCarta and Kegg Pathways on CGAP (Cancer Genome Anatomy Project) plus Links to more Pathways.
• Science NetWatch - interesting science Web sites selected from the Science Magazine