On the Structure of RNA Branching Polytopes

DOI10.1137/17M1144076zbMath1401.92153arXiv1708.05554OpenAlexW2963195334MaRDI QIDQ4554590

Svetlana Poznanović, Christine E. Heitsch, Fidel Barrera-Cruz

Publication date: 9 November 2018

Published in: SIAM Journal on Applied Algebra and Geometry (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1708.05554

zbMATH Keywords

parametric optimizationpolytopemultibranch loopsRNA secondary structure

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Uses Software

• Mfold
• NNDB
• uShuffle

Cites Work

• Unnamed Item
• Parametric analysis of RNA branching configurations
• On some new sequences generalizing the Catalan and Motzkin numbers
• Parametric optimization of sequence alignment
• Geometric combinatorics and computational molecular biology: Branching polytopes for RNA sequences
• Algorithms for Loop Matchings
• Parametric inference for biological sequence analysis
• Algebraic Statistics for Computational Biology