#bioinformatics #rna #secondary-structure

bin+lib rna-ss-params

“rna-ss-params”, Library of RNA secondary structure parameters

21 releases

Uses old Rust 2015

0.1.20 Jan 30, 2021
0.1.18 Dec 4, 2020
0.1.17 May 24, 2020
0.1.16 Mar 4, 2020
0.1.11 Mar 19, 2018

#248 in Science

Download history 10/week @ 2021-05-27 14/week @ 2021-06-03 33/week @ 2021-06-10 6/week @ 2021-06-17 16/week @ 2021-06-24 12/week @ 2021-07-01 16/week @ 2021-07-08 30/week @ 2021-07-15 11/week @ 2021-07-22 54/week @ 2021-07-29 42/week @ 2021-08-05 42/week @ 2021-08-12 14/week @ 2021-08-19 13/week @ 2021-08-26 1/week @ 2021-09-02 28/week @ 2021-09-09

190 downloads per month
Used in 9 crates (via rna-algos)

MIT license

14MB
2K SLoC

"rna-ss-params", Library of RNA Secondary Structure Parameters

This library provides RNA secondary structure parameters. Current available parameters are of Turner 2004 model or CONTRAfold v2.02 model. Turner 2004 model provides experimentally estimated structure parameters based on nearest neighbor thermodynamics. In contrast, CONTRAfold v2.02 model provides secondary structure parameters computationally optimized by maximizing the log likelihood of training secondary structures. My implementation of CONTRAfold v2.02 model is just the copy of the CONTRAfold source code, pre-trained by CONTRAfold developers decade ago. I will supply the CONTRAfold v2.02 model trained by myself using the databases of recent reference RNA secondary structures (e.g., Rfam and bpRNA-1m).

Author

Heartsh

License

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

Dependencies