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Updated: Jul 13, 2026
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
A general computational model for predicting ribosomal frameshifts in genome sequences.
Yanga Byun1, Sanghoon Moon, Kyungsook Han
1School of Computer Science and Engineering, Inha University, Inchon 402-751, South Korea.
Computers in Biology and Medicine
|August 7, 2007
Summary
FSFinder2 predicts programmed ribosomal frameshifts, enabling gene expression in viruses and bacteria. This powerful tool analyzes general frameshift types across all operating systems.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Programmed ribosomal frameshifting is a key mechanism for synthesizing fusion proteins from overlapping open reading frames in RNA viruses.
- Previous tools like FSFinder were limited to specific operating systems and frameshift types (-1 and +1).
Purpose of the Study:
- To develop a versatile web application and web service, FSFinder2, for predicting all types of programmed ribosomal frameshifts.
- To provide a user-friendly and cross-platform solution for analyzing frameshift-mediated gene expression.
Main Methods:
- Development of a web application and web service (FSFinder2).
- Testing FSFinder2 on Shewanella oneidensis MR-1 to evaluate its frameshift prediction capabilities.
- Analysis of general frameshift types beyond -1 and +1.
Main Results:
- FSFinder2 successfully predicts programmed ribosomal frameshifts of general types.
- The tool was tested on Shewanella oneidensis MR-1, demonstrating its applicability.
- FSFinder2 is the first program capable of identifying general frameshift types.
Conclusions:
- FSFinder2 is a powerful and accessible tool for predicting and analyzing genes that utilize frameshifts.
- The web-based nature of FSFinder2 enhances its utility for researchers across different platforms.
- This advancement facilitates a deeper understanding of frameshift mechanisms in gene expression.
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