Research Article

A Topology Structure Based Outer Membrane Proteins Segment Alignment Method

Table 1

Comparison of alignment accuracy with HHalign. The performances are compared separately within TM segments, non-TM segments, and overall sequence. OMSA achieved the best alignment accuracy in all the fields, and that within the TM segments has significantly surpassed the general alignment program HHalign. It indicates that the segment orientation further improves the alignment for OMPs.

MethodsAcc (%)TM-scoreGDT_TS
TMNon-TMOverallTMNon-TMOverallTMNon-TMOverall

OMSA53.345.150.60.4030.3140.3220.3350.2950.307
HHalign42.942.642.70.2170.2560.2420.2090.2260.216

TM: TM segments; Non-TM: non-TM segments; Acc: accuracy.