miRBooking simulates the stochiometric mode of action of miRNAs.
This page hosts the releases of the C implementation as well as some general information on running the program and interpreting its output.
The miRBooking-scan Web service is now available and propose the exploration of the microtargetome a few cell lines.
Add support for GENCODE-style annotations, fix 3’UTR footprint and speedup vacancy calculation in the 5’ direction.
This release bring some build convenience, a standardized floats format (6 digits) and introduce a permissive MIT license.
More efficient computation of sequence index and fix issues with variable-length seed.
mirna_quantitycolumn in the TSV output.
This release backport some changes from the trunk and stabilize the C/Python API.
- Provide and reorganize a more detailed output with common names and vacancy.
- Add Pandas-based helper to the Python API to manipulate the output as a dataframe.
- Drop the
mirbooking-aggregatetool considering that we now have a Pandas-friendly API.
Few memory and CPU time optimizations and add
Initial release with a identical reimplementation of the Java version.
- score table (sha256)
This is passed via the
--score-tableflag and provides hybridization probabilities of all heptamer duplexes. It also possible to generate a custom table.
- 𝚫G° scores (sha256)
This table contains heptamer minimum free energy instead of probabilities. (required for >=1.3.0) Note that the table below simply offer a trade-off between computational time and accuracy. After a certain number of mismatches, the duplex is simply not feasible and will not affect the final solution.
- 𝚫G° scores (2 mismatches) (sha256)
- 𝚫G° scores (3 mismatches) (sha256)
- 𝚫G° scores (4 mismatches) (sha256)
- We have some quantified cell lines from publicly available data.
- C API documentation
Weill, Nathanaël, Lisi Véronique, Scott Nicolas, Dallaire Paul, Pelloux Julie, Major François. “MiRBooking simulates the stoichiometric mode of action of microRNAs”, Nucleic Acids Research 43, no. 14 (2015): 0305-1048, 1362-4962. 10.1093/nar/gkv619.