Harvard Medical School

Laboratory of Reproductive Biology 




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LRB - Bioinformatics Tools

BoxshadeLite is an alignment analyzer.  It parses Clustal .aln files into various Boxshade views.
  • Pretty Alignment:  CLUSTAL alignment viewed as a continuous
    string as opposed to block format
  • Boxshade:  Hightlights Base and Amino Acid differences
  • Hypermutation List: Provides a list of the base number and codon of each G to
    A hypermutation.
  • G to A Hypermutation Boxshade:  Highlights G to A transitions only
  • A to G Hypermutation Boxshade:  Highlights A to G transitions only


HIV Envelope V3 Loop Viral Tropism Predictor.
  • A pairwise alignment is performed using the North American V3 Loop consensus and the input Amino Acid sequence.
  • A prediction is made based on the Charge Rule, which evaluates the relative positions 11 and 25 of the input sequence for the positively charged Amino Acids Lysine and Arginine. The V3 Loop sequence is then predicted to be either SI X4 or NSI R5 type virus.