Molecular Biology Web Resources

Comprehensive Resources Educational Resources Genome Databases Gene & Gene Expression Methods and Protocols Nucleotide Sequences

Protein Sequences, Structures & Family Taxonomy Biological Culture and Stock Collection Databases

Comprehensive Resources

• Databases
  • Entrez Databases (NCBI)
  • UCSC Genome Browser (UCSC) | Tutorial
• Directories
  • Data Analysis Tools (NCBI) contains links to nucleotide and protein sequencing tools.
  • Entrez Genome Centers and Databases (NCBI) is a directory listing of Genome Centers.
  • ExPASy Bioinformatics Resource Portal (Swiss Institute of Bioinformatics) contains links to protein sequence, 3D structure and 2D-gel analytical tools.
• Sitemaps
  • NCBI Sitemap
  • Wellcome Trust Sanger Institute Sitemap

Educational Resources

• Books
  • Brock biology of microorganisms by Michael T. Madigan (UCB Bioscience Library Reserve, QR41.2.B77 2009)
  • Genetics : from genes to genomes by Leland H. Hartwell (UCB Bioscience Library Reserve, QH430.G458 2008)
  • Introduction to bioinformatics by Arthur M. Lesk (UCB Bioscience Library, QH507.L47 2008)
  • Molecular biology of the cell by Bruce Alberts (UCB Bioscience Library Reserve, QH581.2.M64 2008, also available online in 2002 edition on PubMed Bookshelf)
  • Molecular cell biology by Harvey Lodish (UCB Bioscience Library Reserve, QH581.2.M655 2008, also available online in 1999 edition on PubMed Bookshelf)
  • UCB Bioscience Libray Electronic Books
  • PubMed Bookshelf
• Tutorials
• BLAST Sequence Analysis Tool (from the NCBI Handbook)
• Bioinformatics Tools Tutorials (EMBL-EBI)
• NCBI Mini-Courses (NCBI) - 2.5 hours of online course
• UCSC Genome Browser Tutorial (OpenHelix)
• Video Tutorials on Bioinformatics tools (Harvard)
• A Science Primer (NCBI) - a comprehensive guide to Bioinformatics

Genome Databases

• Entrez Genome (NCBI) provides access to over 800 completed genomes.
• Entrez Map Viewer (NCBI) provides genome mapping by chromosomal position, with the integration of genetic and physical maps.
• ENSEMBL Browser (EMBL-EBI-Sanger) provides automated genome annotation and subsequent visualisation of eukaryotic genomes.
• UCSC Genome Browser (UC Santa Cruz) contains reference sequence and working draft assemblies for a large collection of genomes.

• Human
  • Online Mendelian Inheritance in Man - OMIM (NCBI) | Tutorial
  • Human Genome Map Viewer (NCBI]) | Tutorial
• Microbes
• TIGR's Comprehensive Microbial Resources (J. Craig Venter Institute) provides access to all completed, publicly available, prokaryotic genome sequences.
• Integrated Microbial Genomes (Joint Genome Institute) provides access to genomes of bacteria and viruses, plus some genomes from archaea and lower eukaryotes (fungi, yeast).
• The Universal Virus Database (ICTVdB) is an Index of approved virus names linked to virus descriptions.
• Plants
  • Arabidopsis Information Resource (Stanford)
  • MaizeGDB: Maize Genome Database (funded by USDA/ARS)
  • ChromDB Plant chromatin database (University of Arizona)
  • Plant Genomes Central (NCBI)
• Vertebrates
  • VAGA: The Vertebrate Genome Annotation Database includes species information on Homo sapiens, Mus musculus, Danio rerio, Sus scrofa, and Canis familiaris.
• Others
  • Model Organism Databases with links to Arabidopsis, Drosophila, C. elegans, Human, Mouse, Rat, Prokaryotes, and Yeasts.
  • PhyloFacts Phylogenomic encyclopedias of protein families across the tree of life (UC Berkeley)
  • Berkeley Drosophila Genome Project
  • C. elegans Database (EMBL-EBI)
  • euGenes Genetic information for eukaryotic organisms (University of Indiana)
  • FlyBase Drosophila genome (University of Indiana) | Tutorial
  • GBASE Genome database of the mouse
  • SGD: Saccharomyces genome database | Tutorial
  • TGD: Tetrahymena Genome Database
  • WormBase | Tutorial

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