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

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Presentation on theme: "Accuracy of structure-based sequence alignment of automatic (structure-alignment) methods Changhoon Kim and BK Lee Laboratory of Molecular Biology CCR/NCI/NIH."— Presentation transcript:

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)
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
CDD alignment CE alignment DaliLite alignment

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