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 programsselected 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

ly)(superfami node CDD aover averaged )()(

alignment reference in the residues aligned

residues touperror shift with residues alignedcorrectly )(

kfkF

kkf

CARCAR

CAR

=

=N

N

Maximum allowed shift error

Ave

rage

FC

AR

Average fraction of correctly aligned residues (Average FCAR)

Sequence similarity dependenceof Average FCAR(0)

Sequence similarity (% identity)

Ave

rage

FC

AR(0

)

Num

ber

of s

uper

fam

ilies

Alignments sorted by fCAR(0) within each superfamily

Cor

rect

ly a

ligne

d fr

actio

ns (f C

AR)

Variation of fCAR for individual structure pairs

CDD alignment CE alignment DaliLite alignment

An example of alignment errors