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Table 1 FIRE scores

From: Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

Set

Data sets aligned

#ω

FIRE score

1

*metazoan MYB1 and protozoan MYB1

ω ≤ 0.2

0.93

2

*metazoan MYB1 and metazoan MYB2

ω ≤ 0.3

0.94

3

protozoan MYB1 and metazoan MYB2

ω ≤ 0.3

0.99

4

*metazoan GK and protozoan GK

ω ≤ 1.3

+0.62

5

€κ light chain VR and κ light chain VR

ω ≤ 7.0

0.66

6

*κ light chain VR and λ light chain VR

ω ≤ 8.2

0.65

7

*metazoan MYB1 and metazoan p53

ω ≤ 1.3

0.45

8

metazoan MYB1 and metazoan GK

ω ≤ 1.3

0.09

9

κ light chain VR and metazoan p53

ω ≤ 7.0

0.29

10

*metazoan p53 and λ light chain VR

ω ≤ 8.2

0.32

  1. The results of 10 FIRE alignments of the ω MLEs derived from two sequence sets are shown. The range of ω MLEs at codon sites (#) includes values for both data sets, and was taken from model M3 results. FIRE plots and alignments for sets marked with asterisk (*) are provided in Figure 1 and additional file 3, respectively. The two κ data sets (labeled €) represent different κ sequences. Metazoan and protozoan GK data sets differed by >100 codons and therefore produced a relatively low FIRE alignment score (+). DNA-binding domains were used for MYB and p53 alignments. Sets 7-10 are negative controls. GK = glycerol kinase; VR = variable region.