PIRAT

Python3 Implementations of RNA Algorithms & uTilities

Implemented algorithms

Nussinov.py - Nussinov algorithm (https://doi.org/10.1073/pnas.77.11.6309)

Helpful sources

https://rna.informatik.uni-freiburg.de/Teaching/ (https://doi.org/10.1093/nar/gky329)

TODO

Hungarian algorithm

Edmonds algorithm

Kabshch algorithm

Wuchty1999

Sankoff algorithm

Number of structures

Turner algorithm

McCaskill algorithm

pmcomp pmmulti (10.1093/bioinformatics/bth229)

SCFG

MDS, SMACOF, BFSG

Hidden Markov Models

Global/Local Alignment

Tree edit & Tree alignment

Furier transformations

bpseq <-> ct <-> dbn

pdb mmcif