Some terminology

Common similarities between sequences/structures:

• pattern, motif, fingerprint, template, fragment, core, site, alignment, weight matrix, profile…

• “Pattern”: description of structure properties

  • (Deterministic) Decide if a protein matches it or not
  • (Probabilistic) Assign a value to the match

• “Motif” - pattern with biological meaning

Adapted from: Eidhammer, Jonassen & Taylor, “Structure Comparison and Structure Patterns”, JCB, 7:5 pp 685-716, 2000.

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