Related Experiment Video
Updated: Dec 10, 2025
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
4.0K
rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output
Marek Schwarz1, Jiří Vohradský1, Martin Modrák1
1Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia.
Frontiers in Genetics
|August 28, 2020
Summary
rboAnalyzer enhances bioinformatics sequence searches by extending partial RNA matches into full-length sequences. This tool improves homology identification and secondary structure prediction for non-coding RNAs.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence similarity searching is crucial in bioinformatics, especially for non-coding RNAs.
- Interpreting BLAST results can be challenging due to partial sequence matches.
Purpose of the Study:
- To develop rboAnalyzer, a tool for improved interpretation of sequence search results.
- To address the challenge of partial matches in bioinformatics sequence analysis.
Main Methods:
- Extending partial sequence matches to plausible full-length sequences.
- Predicting RNA homology and pooling information from search results and databases like Rfam.
- Generating a rich graphical output for contextualizing matches.
Main Results:
- rboAnalyzer successfully extends partial matches to full-length sequences.
- Improved secondary structure prediction using full-length matches.
- Robust identification of RNA homology and reliable characterization of non-coding RNAs.
Conclusions:
- rboAnalyzer provides a robust method for interpreting sequence search results, particularly for non-coding RNAs.
- The tool enhances secondary structure prediction and homology identification through its analytical capabilities.
- rboAnalyzer facilitates reliable characterization of RNA sequences in BLAST outputs.
Related Concept Videos
02:24Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K
03:21RNA-seq
11.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.4K
01:56Riboswitches
9.3K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
9.3K