Table 1.
The default values of the parameters used in miRanalyzer are shown
| General parameters | ||
|---|---|---|
| Name | Description | Value |
| minLength | The minimum read length, all others will be removed | 17 |
| maxLength | The maximum read length, all reads will be trimmed to this length | 26 |
| Bowtie parameters | ||||
|---|---|---|---|---|
| Name | Description | miRBase | Trans. libraries | Genome |
| −k | Max. number of reported alignments | 10 | 20 | 6 |
| −l | The seed length | 17 | 20 | 17 |
| −n | The number of mismatches within the seed | 1 | 1 | 1 |
| Prediction parameters | ||
|---|---|---|
| Name | Description | Value |
| Score | The posterior probability that the candidate is a true microRNA | 0.9 |
| minNoPositives | miRanalyzer predicts using five models (five different negative sets). This parameter determines the minimum number of models which predicts a candidate to be a new microRNA (default: 3). | 3 |
The web server version allows the user to change the ‘−n’ parameter. The standalone version allows manipulating all of them. We used −l 17 to detect known microRNAs and predict new microRNAs (align to the genome) as this is the shortest microRNA length in miRBase but −l 20 for the other libraries.