Sequence Analysis on the WWW

• ORF Search and Translation Program (Rahul Karnik '00) - run on PC Java 1.1 enabled
  
• Input a DNA sequence, translate it, make a mutation, and see new protein sequence
  
• Simple Modular Architecture Research Tool - search for proteins with specific combinations of domains in defined taxonomic range
  
• Multiple Sequence Alignment (UK)
  • ClustalW Help
    
• The PredictProtein server
  
• Use GenMark to find Exon/Introns
  
• ExPASy Molecular Software - Very Powerful Analysis Tools
  
• Use JavaScript to translate any DNA sequence and mutations of your choice
  
• Use Gene Mark to find Exon/Introns - Mark Borodovsky's free programs that
  have species specific codon bias built in
  
• Center for Biological Sequence Analysis
  
• Form for Multiple Sequence Alignment (USA)
  
• Blocks Search Program Blocks are multiply aligned ungapped amino acid segments corresponding to the most highly conserved regions of proteins.
  
• Web Site to Align Multiple Sequences at Washington Univ. in St. Louis
  
• Sequence Analysis Applets - University of New Hampshire
  
• Virtual Genome Center molecular programs your can run at Univ. Minnesota (Golden Goffers!)
  
• UW Pathology Cytogenetics Resources Genome Project Related Tools