#bioinformatics #rna #secondary-structure

bin+lib rna-ss-params

Library of RNA secondary structure parameters

24 releases

Uses old Rust 2015

new 0.1.23 Jan 30, 2023
0.1.22 Mar 16, 2022
0.1.21 Feb 15, 2022
0.1.20 Jan 30, 2021
0.1.11 Mar 19, 2018

#354 in Science

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239 downloads per month
Used in 11 crates (via rna-algos)

MIT license

18MB
1M SLoC

Library of RNA Secondary Structure Parameters

This library provides tuned computational parameters for RNA secondary structures. Available current parameters are from the Turner 2004 model or the CONTRAfold v2.02 model. The Turner 2004 model provides experimentally estimated structure parameters. (They are based on nearest-neighbor thermodynamics.) In contrast, the CONTRAfold v2.02 model provides secondary structure parameters computationally optimized by maximizing the log-likelihood of training secondary structures. My implementation of the CONTRAfold v2.02 model is just the copy of the CONTRAfold source code, pre-trained by CONTRAfold developers a decade ago. The comparison between the Turner 2004 model and the CONTRAfold v2.02 model is as below:

Model Turner CONTRAfold
Model simpleness Complex Simple
Parameter optimization Wet & dry Dry only
Are RNA loop structures captured? Yes Yes
Are noncanonical base-pairings allowed? No Yes (but they are disabled in this repository)

Author

Heartsh

License

Copyright (c) 2017 Heartsh
Licensed under the MIT license.

Dependencies