Tools & Therapeutics
MarathonRT was discovered by Chen Zhao and developed by Li-Tao Guo when they were members of the Pyle lab. It is an ultraprocessive reverse-transcriptase that moves rapidly through long, highly structured RNAs. It can be obtained from RNAConnect. Anna Pyle is a founder and advisor to RNAConnect.
Lab members Andrew Kohlway, Dahai Luo and Steve Ding demonstrated that short, triphosphorylated stem-loop RNAs are potent inducers of the RIG-I receptor, making them valuable tools for studying and treating viral infections. To develop SLRs, Anna Pyle teamed up with Akiko Iwasaki to found RIGImmune. Anna Pyle is a founder and advisor to the company.
Software & Computational Tools
The Pyle Lab has developed a variety of programs to complement our experimental projects. These software and tools can be used for a variety of RNA sequence, structure, and modification predictions and analyses.
Please visit our GitHub page to download available programs
Some of our tools also have web servers!
MRTModSeq
Author: Rafael de Cesaris Araujo Tavares, Gandhar Mahadeshwar, & Han Wan
Description: Rapid detection of RNA modifications with MarathonRT.
Reference: Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. bioRxiv, 2023
Arena
Author: Zion Perry & Chengxin Zhang
Description: Full atomic reconstruction of RNA structures from coarse-grained representations.
Reference: Perry ZR, Pyle AM, Zhang C. Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models. J Mol Biol, 2023
RSCanner
Author: Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, & Zion Perry
Description: Rapid visualization of RNA secondary structure content across a transcript.
Reference: Mahadeshwar G, Araujo Tavares RC, Wan H, Perry ZR, Pyle AM. RSCanner: rapid assessment and visualization of RNA structure content. Bioinformatics, 2023
rMSA
Author: Chengxin Zhang
Description: RNA sequence database search and multiple sequence alignment generation.
Reference: Zhang C, Zhang Y, Pyle AM. rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. J Mol Biol, 2022
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 and Zhang C, Pyle AM. A unified approach to sequential and non-sequential structure alignment of proteins, RNAs and DNAs. iScience, 2022
CSSR
Author: Chengxin Zhang
Description: CSSR assigns RNA secondary structure to coarse-grained tertiary structure.
Reference: Zhang C and Pyle AM. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. Acta Cryst D, 2022.
