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Research Tools

The Whitehead DNA and Genomic Analysis page The Whitehead Protein Sequence Analysis and Searches page DNA/Protein Analysis Plasmid Maps and Sequences Technical Tips and Protocols - general tips, immunocytochemistry, cDNA libraries Bio/Chemical Vendors and Companies

 

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DNA/Protein Analysis

• Database Searching- Medline, Genbank, and Taxonomy searches
  
  
• Retrieve sequence files (Sive lab only)
  
  
• Detailed restriction endonuclease information from NEB
  
  
• Entrez Search System - nucleotide, protein, structure, and medline searches
  
  
• BLAST
  
  
• ORF finder - This tool identifies all open reading frames in a user's sequence or in a sequence already in the database.
  
  
• PSORT: Prediction of protein sorting signals and localization sites in amino acid sequences
  
  
• TRANSFAC database-Search for artificial or consensus DNA binding sites of known transcription factors
  
  
• Zebrafish Codon Usage from the Japanese DNA Information and Stock Center
  
  
• Xenopus codon usage from the Japanese DNA Information and Stock Center or Harvard
  
  
• Homeobox Gene Classification

Plasmid Maps and Sequences

• NEB Vector Maps and Sequences
  
  
• BD Pharmingen Vectors
  
  
• Promega Vectors
  
  
• Stratagene Vectors
  
  
• Xenopus expression plasmid listings in the XMMR including CS2+, pXEX, pT7TS, pSP64T and more
  
  
• GFP and BFP plasmid maps based on CS2-MT from the Klymkowski Lab Plasmid Map Page
  
  
• Xenopus cDNA probes and expression constructs from the Moon Lab
  
  
• Zebrafish cDNA probes and expression constructs from the Moon Lab
  
  
• Commonly used Xenopus expression vectors, promoter constructs, and misc. genes - also from the Moon lab (CS2, pSP64T, T7TS, CSKA, prolactin, ras, etc)

Technical Tips and Information

• Xenopus Research Tips and Resources
  
  
• Zebrafish Research Tips and Resources
  
  
• Biotechniques Newsgroup archive
  
  
• Biotechniques (Biotechnet)
  
  
• Elsevier Technical Tips Online- technical tips published in Trends in Genetics and other Elsevier journals (as well as new ones) with links to reagent vendors. See "microscopy" for in situ protocols. Note: You have to register to use this service (it's free).
  
  
• For information on antibodies against developmentally important proteins (including Hox proteins), fluorescence tools (with handbook), enzyme substrates, GFP, restriction enzymes or other chemicals see Vendors and Companies below.
  
  
  • The Antibody Resource Page
  • Immunostaining protocols from Vector Labs
  • Biomeda's tips for immunoperoxidase staining
  • Antibodies in the DSHB that are listed under Xenopus or amphibians
  • Xenopus protocols : in situs and immunohistochemistry
  • Monoclonal zebrafish antibodies available from the University of Oregon
  • Histological techniques in Zebrafish (from the Zebrafish Book)
  • Moon lab antibody list
  • XMMR antibody/probe list - see listings "By Marker"
    
    
• cDNA libraries
  
  
  • Xenopus cDNA libraries listed at the XMMR
  • Zebrafish cDNA and genomic libraries

Bio/Chemical Vendors and Companies

• Infoseek list of Biotech companies
  
  
• Biosupply Net - find anything you need
  
  
• Enzyme substrates/fluorescent chemicals
  
  
  • Molecular Probes-fluorescent tools, and a very useful handbook
  • Biosynth - many different substrates for alkaline phosphatase, b-galactosidase, luciferase.
  • Vector Labs - many substrates for AP and peroxidase, immunocytochemistry kits and protocols
  • Clontech GFP manual
    
    
• Antibodies
  
  • Developmental Studies Hybridoma Bank (DSHB)
  • Affinity Bioreagents-antibodies to signal transduction molecules, receptors, transcription factors and much more
    
    
• ATCC
  
  
• Roche/Boehringer-Mannheim
  
  
• Invitrogen
  
  
• NEB - Restriction Enzyme Info, Plasmid and Vector Maps
  
  
• Promega
  
  
• Sigma-Aldrich
  
  
• Stratagene
  
  
• VWR