PPT Slide

Why all these alignments? Genomes are:

• Chemo-physically special
  • Genomic sequences are special – not random: fold, stable, lots of secondary structure & are functional -> Chemo-physically special.
  • Protein Superfamilies share little sequence similarity but have similar 3D structures and may be detectable by sophisticated alignment methods such as ‘threading’.
• Taxonomically/evolutionarily related
  • Genomes consist of a finite set of distinct protein families.
  • Protein families are defined to display close sequence similarity due to a taxonomic/evolutionary relationship indicating shared:
  • • Basic Function
    • Structure
    • Folding
  • 
    So we can suggest a basic function for our ‘query’ sequence if there is a good match (‘hit’ or ‘target’) in the databases with functional ‘annotation’ and/or a 3D structure. At the very least good matches across taxa suggest functional importance of the query gene.

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