Resources

General Bioinformatics Databases

• Bioinformatics Software
• Bioinformatics Database Links  
  Links to many useful molecular resources tools and databases, including bioinformatics sites: This is where you might go to browse and find if there are any new programs or databases that might be helpful for you.
• Nucleic Acids Research Part One & Part Two
  Review of websites and databases: This is updated annually and provides a short summary of what is available at various databases and webservers.
• Sequence Manipulation Suite
  Software available for use on your desktops that allows for some basic manipulations of sequence information.

Literature Search Engines

• PubMed
  National Center for Biological Information database and tools.
• PubChem
  Search engine provides information on the biological activities of small molecules. Search by compound (using name, synonyms or keywords), bioassay descriptions, chemical structure, etc.
• Brenda
  Enzymes database.

Tools for Lab Work

• ExPASy Proteomics Tool
  A massive repository of analytical tools useful for all types of experimental work with proteins.
• E. Coli Codon Usage Analyzer
  Analysis for optimizing protein expression.
• OligCalc
  Calculates oligonucleotide properties. Useful for designing cloning primers.
• Peptide Properties Calculator
  Protein Properties Calculator (extinction coefficients, molecular weights, etc.).

Structural Databases

• RCSB Protein Data Bank
  Main repository for protein structural data.
• Protein Data Bank (Europe)
  Includes structural biology tools and applications.
• Chimera 3D
  Macromolecule structure viewer download and homepage.
• Swiss PDB viewer
  3D viewer similar to Chimera with some additional structure comparison features.

Proteomics

• ExPASy
  ExPASy Proteomics Tool. A massive repository of analytical tools useful for all types of experimental work with proteins.
• BLAST Basic Local Alignment Search Tool
  Protein and gene sequence homology alignments.
• CLUSTALW
  Web-based sequence alignment tool.
• STRING
  Analysis tools for predicting protein-protein interactions and biochemical pathways.

Genomics

• The SEED
  An annotation tool for detailed comparative genome analysis.
• Kyoto Encyclopedia of Genes and Genomes
  A massive repository of protein function data, organized by type of data needed (such as pathway, orthology, genome, ligand).
• J Craig Venter Institute
  Institute for genomic research.
• ENTREZ Genome Project
  List of genomes being sequenced and their status: This is about as complete as we can find and provides useful links, status reports and contact information for various genome projects.
• Gene Expression Omnibus
  A repository of data collected from microarray/gene expression profiling experiments.

 Biochemical Pathways Analysis

• University of Minnesota Biocatalysis/Biodegredation Database
  Predicts microbial biocatalytic reactions and degradation pathways for novel compounds, with links to known pathways.
• Kyoto Encyclopedia of Genes and Genomes
  A massive repository of protein function data, organized by type of data needed (such as pathway, orthology, genome, ligand).

Phylogenetics

• Phylogenetics Pipeline
  This is a useful website that allows one to go from a list of concatenated FASTA files to a phylogenetic tree, all in one, easy to use format.

Model Organisms Database

• E. coli
• S. cerevisiae
• C. elegans
• D. melanogaster
• Human genetic mutations database

Contact Wooster

Biochemistry & Molecular Biol

Severance Hall
943 College Mall
Wooster, OH 44691
Phone: 330-263-2418