[Github repositories for Pyle lab software]
RNA Secondary Structures
HCV Secondary Structure
Reference: Pirakitikulr N, Kohlway A, Lindenbach BD and Pyle AM. The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures. Mol Cell 2016 (62) : 111-120
Download: HCV structure
HOTAIR Secondary Structure
Reference: Somarowthu S, Legiewicz M, Gazquez IC, Marcia M, Liu F and Pyle AM. HOTAIR forms an intricate and modular secondary structure. Mol Cell 2015 (58) : 353-361
Download: HOTAIR structure
Libraries
Discrete RNA Libraries from Pseudo-Torsional Space.
Author: Elisabeth Humphris
Description: Libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone.
Reference: Humphris E and Pyle AM. Discrete RNA Libraries from Pseudo-Torsional Space. J Mol Biol 2012.
Download: RNA Libraries
Software
MRTModSeq
Author: Rafael de Cesaris Araujo Tavares, Gandhar Mahadeshwar, & Han Wan
Description: Rapid detection of RNA modifications with MarathonRT.
References: Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. bioRxiv 2023
Download instructions: The R scripts and markdown files can be downloaded from Github.
Arena
Author: Zion Perry & Chengxin Zhang
Description: Full atomic reconstruction of RNA structures from coarse-grained representations.
References: Perry ZR, Pyle AM, Zhang C. Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models. J Mol Biol 2023
Download instructions: The source code can be downloaded from Github or the Arena web-server.
RSCanner
Author: Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, & Zion Perry
Description: Rapid visualization of RNA secondary structure content across a transcript.
References: Mahadeshwar G, Araujo Tavares RC, Wan H, Perry ZR, Pyle AM. RSCanner: rapid assessment and visualization of RNA structure content. Bioinformatics, 2023
Download instructions: The R scripts and markdown files can be downloaded from Github.
rMSA
Author: Chengxin Zhang
Description: RNA sequence database search and multiple sequence alignment generation.
References: Zhang C, Zhang Y, Pyle AM. rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. J Mol Biol 2022
Download instructions: The source code can be downloaded from Github or the rMSA web-server.
US-align
Author: Chengxin Zhang
Description: Universal Structure Alignment of RNAs, DNAs, proteins and macromolecule complexes.
References: Zhang C, Shine M, Pyle AM, Zhang Y. US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes. Nat Methods (2022).
Zhang C, Pyle AM. A unified approach to sequential and non-sequential structure alignment of proteins, RNAs and DNAs. iScience 2022
Download instructions: The source code can be downloaded from Github or the US-align web-server.
CSSR
Author: Chengxin Zhang
Description: CSSR assigns RNA secondary structure to coarse-grained tertiary structure.
References: Zhang C and Pyle AM. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures . Acta Cryst D (2022).
Download instructions: The source code and binary executable for Linux, Mac and Windows can be downloaded from Github.
AMIGOS III
Author: Morgan Shine & Chengxin Zhang
Description: AMIGOS III allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures within the PyMOL molecular graphic system.
Download instructions: AMIGOS III is available as a PyMOL plugin at Github. An older version of AMIGOS II is available as a standalone Java applet at Github or through SBGrid.
RCrane
Author: Kevin Keating
Description: RCrane allows for semi-automated building of RNA structure within Coot.
Current version: 1.1 (released September 26, 2012) View changelog
References: Keating KS and Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci USA, 107 (2010) 8177-8182.
Keating KS and Pyle AM. RCrane: Semi-automated RNA model building. Acta Cryst D68: 958-995 (2012).
Download instructions: RCrane is included in Coot. Once Coot is launched, go to Extensions -> RCrane launch. RCrane will then be accessible through the newly-created RCrane menu. Coot downloads are available for Linux, Windows, and Mac. The source code for RCrane is available on GitHub.
Note: RCrane and Coot are also available through SBGrid.
Qnifft
Description: Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids.
Qnifft 1.4/2.2
Kim Sharp has developed an updated version of Qnifft that can be compiled for both Linux and SGI platforms. This program is available from his website.
Qnifft 1.2
SHEVEK
Author: Phillip S. Pang
Description: SHEVEK predicts long-range tertiary interactions within RNAs, between RNA-protein and protein-protein interactions from sequence alignments.
Reference: "Prediction of Functional Tertiary Interactions and Intermolecular Interfaces From Primary Sequence Data", PS Pang, E Jankowsky, LM Wadley and AM Pyle, J of Experimental Zoology (Mol Dev Evol) (2005), 000, 1-14.
Download instructions: SHEVEK is available on Github.
Old Versions of Software
