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Table 1 Pairwise sequence alignment performance evaluated on the BAliBASE 3.0 benchmark.

From: Sequence alignment by passing messages

Ref

Pair-HMM

   

Message-Passing

   
    

λ= 0.25

λ= 0.50

λ= 0.75

 

SN

PPV

CPU

SN

PPV

CPU

SN

PPV

CPU

SN

PPV

CPU

RV11

0.048

0.106

1.934

0.123

0.149

0.769

0.155

0.175

1.465

0.198

0.209

3.675

RV12

0.213

0.414

2.707

0.399

0.468

1.146

0.475

0.523

2.145

0.569

0.595

5.200

RV20

0.276

0.476

2.725

0.504

0.568

1.186

0.570

0.613

2.251

0.643

0.665

5.531

RV30

0.168

0.300

2.656

0.324

0.369

1.143

0.372

0.402

2.160

0.426

0.441

5.432

RV40

0.153

0.271

4.084

0.250

0.284

1.760

0.300

0.323

3.234

0.361

0.373

7.970

RV50

0.140

0.254

4.969

0.248

0.278

2.102

0.294

0.312

3.967

0.348

0.353

9.856

  1. The average sensitivity (SN), positive predictive value (PPV), and CPU time (seconds) on different reference sets are shown for each sequence alignment scheme. All experiments were performed in Matlab on a MacPro workstation with 2 × 2.8 GHz Quad-Core Intel Xeon processors and 32GB memory.
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BMC Genomics

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