RNA interaction format: a general data format for RNA interactions-Reference-Cited by-同舟云学术

RNA interaction format: a general data format for RNA interactions

Published:2023-11-01 Issue:11 Volume:39 Page:
ISSN:1367-4811
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Schäfer Richard A¹^ORCID,Rabsch Dominik²,Scholz Guillaume E³,Stadler Peter F³^ORCID,Hess Wolfgang R⁴,Backofen Rolf²^ORCID,Fallmann Jörg³,Voß Björn¹^ORCID

Affiliation:

1. RNA-Biology and Bioinformatics, Institute of Biomedical Genetics, University of Stuttgart , Allmandring 31 , 70569 Stuttgart, Germany

2. Bioinformatics Group, Department of Computer Science, University of Freiburg , Georges-Köhler-Allee 106 , 79110 Freiburg, Germany

3. Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig , Härtelstr. 16-18 , 04107 Leipzig, Germany

4. Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg , Schänzlestr. 1 , 79104 Freiburg, Germany

Abstract

Abstract Summary RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardized data format that can capture the nature of all these different interactions in detail. Availability and implementation Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA–RNA and RNA–Protein interactions and provide reference implementations in C/C++, Python, and JavaScript. RIF is released under licence GNU General Public License version 3 (GNU GPLv3) and is available on https://github.com/RNABioInfo/rna-interaction-format.

Funder

German Ministry of Education and Research

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad665/53000531/btad665.pdf

Reference18 articles.

1. PEPPI: whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning;Bell;J Mol Biol,2022

2. Partition function and base pairing probabilities of RNA heterodimers;Bernhart;Algorithms Mol Biol,2006

3. snoDB: an interactive database of human snoRNA sequences, abundance and interactions;Bouchard-Bourelle;Nucleic Acids Res,2020

4. GraphML Progress Report Structural Layer Proposal