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Published on: May 19, 2019
PsRNA: a computing engine for the comparative identification of putative small RNA locations within intergenic
Jayavel Sridhar1, Govindaraj Sowmiya, Kanagaraj Sekar
1Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai, India.
Genomics, Proteomics & Bioinformatics
|August 10, 2010
Summary
A new computational tool, PsRNA server, aids in identifying small RNA (sRNA) regions within bacterial genomes. This engine helps annotate un-annotated intergenic regions, improving our understanding of bacterial gene regulation.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Small RNAs (sRNAs) are crucial non-coding molecules regulating cellular functions.
- Identifying sRNAs is challenging due to limited sequence and structural biases.
- Many intergenic regions in bacterial genomes remain un-annotated.
Purpose of the Study:
- To develop a computational engine for identifying and annotating putative small RNA regions.
- To facilitate the discovery of novel sRNAs in Enterobacteriaceae genomes.
- To locate conserved, shuffled, or deleted gene clusters.
Main Methods:
- A computational engine, the PsRNA server, was developed.
- It utilizes known sRNA data and KEGG Orthology (KO) numbers as templates.
- The engine searches intergenic regions in related bacterial genomes.
Main Results:
- The PsRNA server successfully identifies putative sRNA regions.
- It can also detect genomic rearrangements like conserved, shuffled, or deleted gene clusters.
- Increased KO number assignments enhance the tool's sensitivity.
Conclusions:
- The PsRNA server is a valuable tool for discovering and annotating bacterial sRNAs.
- It aids in understanding gene regulation and genomic evolution in bacteria.
- The server is publicly accessible for research use.
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