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Table 1 The features used in HairpinSVM

From: A novel two-layer SVM model in miRNA Drosha processing site detection

ID

Name

Description

1

Length

The length of the sequence

2

Loop_length

The loop size of hairpin structure

3

Stem_length

The stem length of hairpin structure

4

Pair

The number of base pairs in folding result

5

Pair_frac

The fraction of paired base in sequence

7

Insert_count

The number of bulges in the folding structure output by RNAfold

6

Insert_frac

The average length of bulges in sequence

8

Insert_count_frac

The ratio between the nucleotides in bulges and those in the sequence

9

Mfe

The minimal free energy output by RNAfold

10

Ensemble_fe

The free energy of the thermodynamic ensemble

11

Ensemble_fq

The probability of this single structure in the Boltzmann weighted ensemble of all structures.

12

Ensemble_div

The ensemble diversity is the average base-pair distance between all structures in the thermodynamic ensemble.