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Table 3 Average Q scores in pairwise alignment tests with typical substitution matrices.

From: MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues

Matrix

HOMSTRAD (Pairwise only)

Method

0-15%

(25)

15-30%

(207)

30-45%

(173)

All

(630)

PAM250

    

MTRAP

0.421

0.655

0.874

0.817

Needle

0.226

0.548

0.837

0.763

ClustalW2

0.234

0.528

0.817

0.747

BLOSUM62

    

MTRAP

0.410

0.653

0.878

0.817

Needle

0.223

0.556

0.843

0.768

ClustalW2

0.276

0.585

0.861

0.784

GONNET250*

    

MTRAP

0.412

0.659

0.879

0.819

ClustalW2

0.313

0.619

0.867

0.800

  1. The average Q scores of four testing datasets with different identity ranges on HOMSTRAD are shown. The number in parentheses denotes the number of alignments in each sequence identity range. For each sequence identity range, the best scores in each substitution matrix are in bold.
  2. *Needle does not support GONNET matrix.