Calculation Parameters¶
miRanda algorithm used by metaRNA accepts the following optional parameters.
Parameter | Type | Default | Description |
---|---|---|---|
scale | float | 4.0 | The 5’ miRNA scaling parameter. |
strict | int | 0 | Perform a Strict Seed search when set to 1. |
gap_open | float | -9.0 | Gap-open Penalty |
gap_extend | float | -4.0 | Gap-extend Penalty |
score_threshold | float | 50.0 | Score Threshold for reporting hits |
energy_threshold | float | 1.0 | Energy Threshold for reporting hits |
length_5p_for_weighting | int | 8 | The 5’ sequence length to be weighed except for the last residue. |
temperature | int | 30 | Used while calculating Free Energy |
alignment_len_threshold | int | 8 | Minimum alignment. |
Passing Parameters¶
The parameters are passed as keyword arguments.
targets = scan(gene_sequence, mirna_sequence, scale=5.0, strict=1)