Table 1 Evaluation of localized alignments. 10395 mouse mRNAs and 2007 zebrafish mRNAs are aligned to the orthologous regions in the human genome.

CDS+UTR (nucl. level)

CDS alone (nucl. level)

CDS alone (exon level)

Speed (mRNA/hr)

Algorithm

Sn

Sp

Sn

Sp

Sn

Sp

CAT

0.765

0.961

0.924

0.968

0.855

0.893

3579

est2genome

0.772

0.963

0.926

0.970

0.856

0.895

17

GeneWise

n/a

n/a

0.927

0.972

0.869

0.917

8

Exonerate

0.385

0.983

0.589

0.977

0.495

0.791

1254

exonerate-aa

n/a

n/a

0.856

0.977

0.787

0.890

10027

BLAT

0.487

0.976

0.678

0.973

0.161

0.172

5138

BLAT-dnax

0.615

0.979

0.872

0.975

0.513

0.518

1172

sim4

0.535

0.977

0.743

0.976

0.524

0.569

36815

Zebrafish mRNA to Human genome

CDS+UTR (nucl. level)

CDS alone (nucl. level)

CDS alone (exon level)

Speed (mRNA/hr)

Algorithm

Sn

Sp

Sn

Sp

Sn

Sp

CAT

0.489

0.963

0.803

0.957

0.645

0.754

2806

est2genome

0.463

0.968

0.764

0.961

0.590

0.750

41

GeneWise

n/a

n/a

0.862

0.975

0.781

0.879

12

exonerate-aa

n/a

n/a

0.652

0.975

0.543

0.772

6757