#bioinformatics #rna #secondary-structure

bin+lib rna-algos

Library of RNA Bioinformatics Algorithms

37 releases

Uses old Rust 2015

new 0.1.36 Jan 31, 2023
0.1.35 Nov 23, 2022
0.1.34 Sep 17, 2022
0.1.32 Jun 19, 2022
0.1.6 Mar 19, 2018

#450 in Science

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Used in 10 crates (4 directly)

MIT license

4MB
3K SLoC

Rust 2.5K SLoC // 0.0% comments Python 432 SLoC // 0.0% comments

Library of RNA Bioinformatics Algorithms

This library provides basic algorithms in RNA bioinformatics. Available current algorithms are the gamma-centroid structure estimator, McCaskill's algorithm, and Durbin's algorithm. To model RNA secondary structure scoring, the Turner 2004 model and the CONTRAfold v2.02 model are available. More descriptions of these two scoring models are here. I adopt the CONTRAlign v2.01 model to model RNA sequence alignment scoring. The gamma-centroid structure estimator of this repository is compared to that of CentroidFold regarding secondary structure prediction accuracy:

Gamma-centroid estimator performance of different models and different implementations

Author

Heartsh

License

Copyright (c) 2018 Heartsh
Licensed under the MIT license.

Dependencies

~31MB
~1.5M SLoC