From: Systematic characterization of small RNAome during zebrafish early developmental stages
No. | Features | Description |
---|---|---|
1 | %(|G| + |C|) | (|G| + |C|) / L * 100, where L is the length of sequence |
2-17 | %XY | |XY| / (L − 1) * 100, where |XY| denotes the number of dinucleotide XY, X,Y ⊂ [A,C,G,U] |
18 | MCPN | Maximum of consecutive paired nucleotides in the secondary structure |
19 | r_p_n | The total number of paired nucleotides / L |
20 | r_unp_n | The total number of unpaired nucleotides / L |
21 | r_p_unp | The total number of paired nucleotides / the total number of unpaired nucleotides |
22 | avg_bp_stem | The total number of base pairs / the total number of stemsa |
23 | dP | The total number of base pairs / L |
24 | n_bulge | The total number of bulgesb |
25 | r_unp_bulge | The total number of unpaired nucleotides / the total number of bulges |
26 | r_bulge_l | The total number of bulges / L |
27-58 | Triplet elements | Triplet structure-sequence elements |
59 | MFE | Calculated using RNAfold under the default parameters |
60 | dG | MFE / L |
61 | MFE1 | (MFE / L) /%(|G| + |C|) |
62 | MFE2 | (MFE / L) / n_stems, where n_stems denotes the number of stems |
63 | MFE3 | (MFE / L) / n_loops, where n_loops denotes the number of loops |
64 | MFE4 | MFE / the total number of base pairs |
65 | MFE5 | (MFE / L) / n_bulges |