AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

BMC Bioinformatics

Table 1 Sensitivity at three levels of error-rate for a few profile-profile search methods.

Method	Sensitivity at 5% error rate	Sensitivity at 10% error rate	Sensitivity at 50% error rate	Source
AlignHUSH	52.5%	57.2% (58.5%*)	66.8%	Current work
HHSearch (with SS)	51%	51.3% (48.8%^§, 54.2%*)	56%	Current work and Soding, 2005 [18]
HHSearch (no SS)	NA	46.7%	NA	Soding, 2005 [18]
PRC	53.2%	54.4% (53.2%*)	58.6%	Current work
PROCAIN	NA	52% ^#	~60% ^#	Wang et al, 2009 [25]
PROF_SIM	NA	24.9%	NA	Soding, 2005 [18]
COMPASS	NA	34.0%	NA	Soding, 2005 [18]

The sensitivity values at three levels of error rates for some of the most commonly used profile-profile search methods. The source of each value is given in the last column. Note that the datasets used and the definitions used for true positives can differ from one source to another and hence the values are not comparable across different sources.
"#": The values given for PROCAIN are extracted from Fig 2b of Wang et al [25] where the definition of true positives and false positives is similar to that used in the current work. "§": Value reported from Soding, 2005 [18]. "*": The values reported with asterisk are for the comparison using the latest SCOP release. For HHSearch the value reported is for the latest version of the program.

ISSN: 1471-2105