CopomuS is a tool for selecting mutation candidate points for sRNA-RNA interactions. For this it takes different measures for evaluating and ranking each position. CopomuS is highly configurable for specific purposes, see below for an explanation of all arguments.
./CopomoS.py -q <query-sequence> -t <target-sequence>
mutation rank qIndex tIndex bpWildtype bpMutated mfeCover_rank mfeCover_ww mfeCover_wm mfeCover_mw mfeCover_mm mfeCover_is_valid E_rank E_ww E_wm E_mw E_mm E_is_valid minDeltaE_rank minDeltaE_wm/ww minDeltaE_mw/ww minDeltaE_wm/mm minDeltaE_mw/mm minDeltaE_ww/mm minDeltaE_min
U4A&A11U 1 4 11 UA AU 1 True False False True 1 1 -9.32 -5.43 -7.25 -8.46 1 3 3.89 2.07 3.03 1.21 -0.86 1.21
C16G&G1C 2 16 1 CG GC 1 True False True True 1 2 -9.32 -8.11 -5.31 -5.99 0 5 1.21 4.01 -2.12 0.68 -3.33 -2.12
G15C&C2G 2 15 2 GC CG 1 True True False True 1 2 -9.32 -12.37 -8.12 -12.2 0 5 -3.05 1.2 -0.17 4.08 2.88 -3.05
...| Flag | Value | Default | Description |
|---|---|---|---|
| -h, --help | Gives detailed command help. | ||
| -q, --query | sequence | Query as a raw sequence. | |
| -t, --target | sequence | Target as a raw sequence. | |
| -m, --measure | {E, ed1, ed2, maxED, mfeCover, mfeOverlap, spotProb, qAccessProfile, tAccessProfile, qEnergyProfile, tEnergyProfile} | E | The measure used to calculate the rank of a base pair. Can be used multiple times. In that case, base pairs are ranked in order of measurements specified. |
| --qIdxPos0 | integer | 1 | (Optional) starting index for the query. |
| --tIdxPos0 | integer | 1 | (Optional) starting index for the target. |
| -c, --candidateSelection | {mfe, mfeSO} | mfe | (Optional) method by which base pair candidates are selected from the sequences. |
| -f, --candidateFilters | {GU, AU, CG, lp, lpMfe, he, heMfe} | None | (Optional) filter by which base pair candidates are filtered. Can be used multiple times to combine filters. |
| -g, --generator | {flip, any} | flip | (Optional) method used to generate mutated sequences by which base pairs are ranked. |
| --mutationEncoding | string (ex. G1C&U7G) | (Optional) allows specific selection of candidates by specifying a mutation encoding. If this option is specified, -c, -f and -g will be ignored. | |
| -o, --output | file name | STDOUT | (Optional) file to which the output should be written to. |
| -d, --delimiter | character | "\t" (tab) | (Optional) delimiter used to separate csv output. |
| -p, --parameterFile | file name | None | (optional) parameter file to be used in IntaRNA calls to further guide predictions. |
| -t, --threads | integer | 0 (all) | (Optional) thread count used by IntaRNA. |
| Name | Description |
|---|---|
| E | (class) Interaction Energy between query and target. |
| minDeltaE | (sort) Energy difference between different combinations of mutation types (ww, wm, mw, mm). |
| mfeCover | (class) Mutation position has to be in MFE. |
| Eqi | (class) Energy profile on query at mutation position. |
| Eti | (class) Energy profile on target at mutation position. |
| EDqi | (sort) Accessibility profile on query at mutation position. |
| cEDqi | (class) Accessibility profile on query at mutation position needs to be constant. |
The default measure combination is -m mfeCover -m E -m minDeltaE.
It is advised to always use a sorting measure at the end, to improve the resolution of the result,
since class measures only split mutations in 3 ranks (valid, invalid, no more interaction).
The choice specified by this argument defines the method, which is used to select candidate base pairs from the given sequences.
| Name | Description |
|---|---|
| mfe | Selects all base pairs from the MFE region. |
| mfeSO | Selects all base pairs from all suboptimal interactions that are in the MFE region. |
The filters filter out base pairs from all candidates that do not comply with the constraints.
| Name | Description |
|---|---|
| GU | Filters out any GU or UG base pairs. |
| AU | Filters out any AU or UA base pairs. |
| GC | Filters out any GC or CG base pairs. |
| lp | Filters lonely base pairs that can not stack (both neighbors not in MFE and both neighbors cant pair). |
| lpMfe | Filters lonely base pairs in MFE interaction (both neighbors not in MFE). |
| he | Filters helix ends (One neighbor can pair, the other one can not). |
| heMfe | Filters helix ends (One neighbor in MFE, the other one is not). |
The mutation generator chooses the method by which mutated sequences are generated.
| Name | Description |
|---|---|
| flip | Flips a base pair to generate the mutated sequences (for example GC --> CG) |
| any | Generates all logical base pair combinations from a given base pair (for example GC --> CG, UG, UA) |