MutationOrder: Most likely order of mutation events in RNA
Determine the most likely order in which single nucleotide mutations happened between two RNA sequences.
Developed to analyse the HAR 1 region.
As long as the two input RNAs are small enough enough (couple hundred nucleotides) and the number of mutations is small enough (around 20-26, since the algorithm is exponential in this number) the algorithm should work for similar problems without changes.
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Modules
[Index]
Flags
Manual Flags
| Name | Description | Default |
|---|---|---|
| debug | Enable bounds checking and various other debug operations at the cost of a significant performance penalty. | Disabled |
| debugoutput | Enable debug output, which spams the screen full of index information | Disabled |
Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info
Downloads
- MutationOrder-0.0.0.1.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
| Versions [RSS] | 0.0.0.1, 0.0.0.2, 0.0.1.0 |
|---|---|
| Change log | changelog.md |
| Dependencies | ADPfusion (>=0.5.2 && <0.5.3), ADPfusionSet (>=0.0.0 && <0.0.1), aeson (>=1.1), base (>=4.7 && <5.0), bimaps (>=0.1.0 && <0.1.1), BiobaseXNA (>=0.9.3 && <0.9.4), bytestring, cereal (>=0.5), cereal-vector (>=0.2), cmdargs (>=0.10), containers, deepseq (>=1.4), directory, DPutils (>=0.0.1 && <0.0.2), filepath, FormalGrammars (>=0.3.1 && <0.3.2), log-domain (>=0.10), MutationOrder, parallel (>=3.2), PrimitiveArray (>=0.8.0 && <0.8.1), PrimitiveArray-Pretty (>=0.0.0 && <0.0.1), serialize-instances (>=0.1), ShortestPathProblems (>=0.0.0 && <0.0.1), text (>=1.0), unordered-containers (>=0.2.7), vector (>=0.11), vector-strategies (>=0.4), ViennaRNA-bindings (>=0.233.1 && <0.233.2), zlib (>=0.6) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2017 |
| Author | Maria Beatriz Walter Costa, Christian Hoener zu Siederdissen, 2017 |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Category | Bioinformatics |
| Home page | https://github.com/choener/MutationOrder |
| Bug tracker | https://github.com/choener/MutationOrder/issues |
| Source repo | head: git clone git://github.com/choener/MutationOrder |
| Uploaded | by ChristianHoener at 2017-03-06T23:07:24Z |
| Distributions | |
| Executables | MutationOrder |
| Downloads | 2461 total (11 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2017-03-06 [all 1 reports] |
Readme for MutationOrder-0.0.0.1
[back to package description]
Determine the most likely order of mutations from one RNA sequence to another.
- Walter Costa, Maria Beatriz and Hoener zu Siederdissen, Christian and Tulpan, Dan and Stadler, Peter F. and Nowick, Katja
Uncovering the Structural Evolution of the Human Accelerated Region 1
2017, submitted
preprint
Usage instructions
We assume that you have two Fasta files, from.fa and to.fa but they can be named however is convenient (say chimp.fa and human.fa). Each file has to contain exactly one sequence and both sequences have to be of the same length.
We then run
./MutationOrder --workdb from-to.json.gz --scoretype pairdistcen --onlypositive --outputprefix test
This will generate test.run, test-edge.eps, and
test-meaorder.eps. The test.run file provides extensive output of
the optimal path, the first-last probabilities, the edge probabilities, and the
mea output. The two eps files give a graphical representation of the edge
probabilities, for the meaorder in order of the path of maximum expected
accuracy.
The --scoretype allows for mfe, centroid, pairdistcen,
and pairdistmfe, which analyse possible evoluationary paths according to
mfe energy, centroid energy, smallest base pair distances for each step in the
centroid or mfe case.
Installation
Follow this link to the bottom of the page. Binaries are available for download and installation from sources via Haskell Stack are described.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/