Computational Molecular Biology and Genomics Projects - Data Sources and Software Tools - Fall 03

Comprehensive data sources

• Pittsburgh Supercomputing Center Sequence Analysis Resource
• National Center for Biotechnology Information (NCBI)
• RNA world
• Microbial genomics gateway
• NIST Engineering Statistics Handbook

Sequence data bases

• NCBI Entrez: Genbank and related data bases.
• The Institute for Genomic Research (TIGR)
• ExPASy (Expert Protein Analysis System): Swiss-Prot and related data bases.
• Microbial Genome Database

Organism specific databases

• Mouse Genome Informatics (Jax)
• Cow
• FlyBase
• C. elegans
• Saccharomyces Genome Database (Yeast)

Genome Browsers

• NCBI Mapviewer
• Ensembl Genome Browser
• USCS Genome Browser

Single Nucleotide Polymorphisms

• The HapMap Project
  
• dbSNP
• JSNP

DNA regulatory motifs

• Databases:
  • Database of Evolutionary Conserved Regions in Vertebrates. Includes transcription factors.
        See also ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes Loots and Ovcharenko, Bioinformatics, 2007.
  • DNA binding-site matrices for 59 known E. coli DNA motifs
  • Motifs found by AlignACE in 17 microbial genomes
  • RegulonDB: a database on transcriptional regulation in Escherichia coli
  • DPInteract database: a database of DNA-binding proteins and their binding sites
  • The Promoter Database of Saccharomyces cerevisiae at Cold Spring Harbor
  • TRANSFAC - The Transcription Factor Database
• Tools:
  • Download the original Gibbs sampler C code
  • Web interface for original Gibbs sampler algorithm
  • Regulatory Sequence Analysis Tools at UNAM
  • Download AlignACE version of Gibbs sampler algorithm
  • MEME: ``Multiple EM for Motif Elicitation''
  • Sequence Pattern Discovery tutorial from ISMB '98: Alvis Brazma & Inge Jonassen
  • Sequence Pattern Discovery Links

Gene Annotation

• Common Orthologous Groups: The COG database
• Gene Ontology Consortium (GO)
• KEGG
• Enzyme Nomenclature
• InterPro Database

Domain Data Bases

• CDART
• Interpro's list of domain data bases

Molecular Structure

• The RNA Structure Database
• Structural Classification of Proteins (SCOP)
• CATH Protein Structure Classification
• Protein Data Bank (PDB)
• NCBI Structure

Pathways and Biological Networks

• A collection of pathway databases
• Signaling Pathway Database (SPAD)
  
• SGD Pathway Tools
• Transcriptional Regulatory Networks in Saccharomyces cerevisiae
  Lee et al., Science. 2002 Oct 25;298(5594):799-804
  

Expression Data

• Gene Expression Omnibus (GEO)
  
• Stanford Array Database
  
• Young Lab Genome-Wide Expression Page
  
• National Cancer Institute
  
  • NCI60 Cancer Microarray Project
  • Genomics and Bioinformatics Group Follow link at bottom of page for data
    
  • NCI 60: Gene Expression Database for the Molecular Pharmacology of Cancer
  • Web Accessible Data and Tools
  • Molecular Target Data
  • Expression Profiling Data: Lymphoma
    A. A. Alizadeh et al., Nature 2000.
  • Biological Testing BranchMostly experimental resources.
    

Protein-Protein interactions

• BIND
• DIP
• Yeast two-hybrid (Fields)
• Yeast two-hybrid (Ito)

Trees

• Tree of Life Web Project
• Ribosomal Database Project II
• Joe Felsenstein's list of phylogeny programs

Protein subcellular localization data.

• CD-Tagging Database