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Table 1 Features used in ZmirP

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

  1. a. A stem contains at least three continuous base pairs; b. A bulge contains at least three adjacent unpaired nucleotides.