Table 3 Class I vs genes: The four most discriminating dinucleotides when comparing the HMM trained on class I TEs and the HMM trained on genes for each state of the HMM. E1, E2, E3 are the three coding states; I is the non-coding state. Log2 of the frequency ratio is given in parentheses. A value of +1 (resp. -1) thus indicates a twofold increase (resp. decrease) of the frequency in the TE model.
From: Detection of transposable elements by their compositional bias
HMM state | A. thaliana | |||
|---|---|---|---|---|
E1 | CG (-0.79) | CC (-0.32) | AC (0.20) | TC (0.17) |
E2 | CA (0.28) | TA (0.26) | AC (0.17) | TC (-0.14) |
E3 | CG (-0.31) | GC (-0.30) | TC (-0.23) | CC (-0.18) |
I | CG (2.23) | CC (1.76) | TT (-1.62) | TA (-1.35) |
HMM state | C. elegans | |||
E1 | TG (-1.71) | CT (1.12) | CC (0.96) | AG (-0.85) |
E2 | GA (-1.66) | GG (-1.17) | TA (0.80) | TC (0.73) |
E3 | TA (1.03) | CC (0.90) | TT (-0.68) | AT (-0.67) |
I | TT (-1.73) | CG (1.22) | TA (-0.87) | CC (0.87) |
HMM state | D. melanogaster | |||
E1 | AG (0.89) | AA (0.87) | TA (0.66) | GG (-0.58) |
E2 | AG (0.59) | TG (0.38) | GA (-0.25) | GG (-0.24) |
E3 | TA (1.06) | CA (0.73) | GG (0.72) | TG (-0.68) |
I | GG (-1.03) | GC (-0.56) | AA (0.55) | CG (-0.51) |