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Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods

Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods. Changhoon Kim and BK Lee Laboratory of Molecular Biology CCR/NCI/NIH. What we did …. Evaluated 7 structure alignment programs selected based on their availability and popularity

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Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods

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  1. Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods Changhoon Kim and BK Lee Laboratory of Molecular Biology CCR/NCI/NIH

  2. What we did … • Evaluated 7 structure alignment programs selected based on their availability and popularity (CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA, VAST) • Standard of truth: NCBI’s CDD alignments Conserved Domain Database is manually procured. Contains only the conserved core residues. • Performance Measure

  3. Average fraction of correctly aligned residues (Average FCAR) Average FCAR Maximum allowed shift error

  4. Sequence similarity dependence of Average FCAR(0) Average FCAR(0) Number of superfamilies Sequence similarity (% identity)

  5. Variation of fCAR for individual structure pairs Correctly aligned fractions (fCAR) Alignments sorted by fCAR(0) within each superfamily

  6. An example of alignment errors CE alignment DaliLite alignment CDD alignment

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