Up: Component summary
Up: Component summary
Component
MEMERunnerFinds enriched motifs from the given set of DNA sequences. This component is a wrapper for Multiple Em for Motif Elicitation (MEME).
| Version | 1.2 |
|---|---|
| Bundle | microarray |
| Categories | Sequence Motif |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | MEME |
| Source files | component.xml MEMERunner.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| sequences | FASTA | Mandatory | A list of input sequencies |
Outputs| Name | Type | Description |
|---|---|---|
| motifs | MotifSet | A set of motifs that were found |
| annot | AnnotationTable | Motif annotations provided by MEME. |
| report | TextFile | MEME output document |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| cpu | int | 1 | Number of parallel processors to be used |
| instDir | string | (no default) | MEME installation folder |
| maxw | int | 15 | Maximum motif width |
| minw | int | 4 | Minumum motif width |
| nmotifs | int | 3 | Maximum number of motifs to find |
| pal | boolean | false | Force palindromes |
| revcomp | boolean | false | Allow sites also on the reverse complement strand |
Test cases| Test case | Parameters▼ | IN sequences |
OUT motifs |
OUT annot |
OUT report |
|
|---|---|---|---|---|---|---|
| case1 | properties | sequences | motifs | annot | (missing) | |
|
instDir=/opt/meme, |
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