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08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
PRFdb: a database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals
Ashton T Belew1, Nicholas L Hepler, Jonathan L Jacobs
1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20854, USA. abelew@umd.edu
BMC Genomics
|July 19, 2008
Summary
The Programmed Ribosomal Frameshift Database (PRFdb) aids researchers in identifying programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes. This database uses algorithms and thermodynamic stability to find these crucial genetic signals.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The Programmed Ribosomal Frameshift Database (PRFdb) offers a tool for identifying programmed -1 ribosomal frameshift (-1 PRF) signals in eukaryotic genes.
- These signals are critical regulatory elements in gene expression.
Purpose of the Study:
- To provide researchers with an accessible interface for detecting potential -1 PRF signals.
- To compile and organize data on -1 PRF signals from various genomic sources.
Main Methods:
- Sequences are imported from whole genomes (e.g., yeast, mammalian).
- Multiple algorithms filter sequences to identify heptameric slippery sites and mRNA pseudoknots characteristic of -1 PRF signals.
- Thermodynamic stability (DeltaG°) of native sequences is compared to randomized sequences to assess signal significance.
Main Results:
- A user-friendly, searchable relational database of potential -1 PRF signals has been created.
- The database facilitates the identification of candidate -1 PRF signals within imported genetic sequences.
Conclusions:
- PRFdb empowers researchers to investigate potential -1 PRF signals in their genes of interest.
- The database serves as a valuable metasource for cross-referencing with other biological databases.
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