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, but agnostic to the
actual sequences and can be used to analyze any RNA sequence
that fits the algorithmic constraints.
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.
We currently only consider point mutations, not in-dels.
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Modules
- BioInf
- BioInf.MutationOrder
- BioInf.MutationOrder.BackMutations
- BioInf.MutationOrder.EdgeProb
- BioInf.MutationOrder.MinDist
- BioInf.MutationOrder.RNA
- BioInf.MutationOrder.SequenceDB
- BioInf.MutationOrder
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-0.0.1.0.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), attoparsec (>=0.13), base (>=4.7 && <5.0), bimaps (>=0.1.0 && <0.1.1), BiobaseXNA (>=0.9.3 && <0.9.4), bytestring, bytestring-trie (>=0.2), cereal (>=0.5), cereal-vector (>=0.2), cmdargs (>=0.10), containers, deepseq (>=1.4), directory, DPutils (>=0.0.1 && <0.0.2), errors (>=2.0), file-embed (>=0.0.8), filemanip (>=0.3), filepath, FormalGrammars (>=0.3.1 && <0.3.2), hashable (>=1.2), lens (>=4.0), log-domain (>=0.10), mtl, MutationOrder, OrderedBits (>=0.0.1 && <0.0.2), 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), split (>=0.2), 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] |
Tested with | ghc ==8.0.2 |
License | GPL-3.0-only |
Copyright | Maria Beatriz Walter Costa, 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 this: git clone git://github.com/choener/MutationOrder/tree/0.0.1.0(tag 0.0.1.0) |
Uploaded | by ChristianHoener at 2017-10-24T21:28:42Z |
Distributions | |
Executables | MutationOrder |
Downloads | 2524 total (6 in the last 30 days) |
Rating | (no votes yet) [estimated by Bayesian average] |
Your Rating | |
Status | Docs not available [build log] Last success reported on 2017-10-24 [all 2 reports] |