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Updated: Jun 20, 2026
09:36
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
Published on: April 10, 2018
Customized strategies for discovering distant ncRNA homologs
Axel Mosig1, Liang Zhu, Peter F Stadler
1Chair of Bioinformatics, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
Briefings in Functional Genomics & Proteomics
|September 26, 2009
Summary
Identifying non-coding RNAs (ncRNAs) is challenging due to their short sequences and conserved motifs. This review explores advanced search tools for homology detection, especially in the difficult
Area of Science:
- Computational Biology
- Bioinformatics
- Genomics
Background:
- Many non-coding RNAs (ncRNAs) are short and/or poorly conserved, complicating homology searches.
- Longer ncRNAs often comprise conserved structural motifs rather than globally conserved secondary structures.
- Existing databases like Rfam face challenges with sparse data, particularly for prokaryotic ncRNA families.
Purpose of the Study:
- To review recent advancements in sequence-based search tools tailored for non-coding RNA (ncRNA) analysis.
- To highlight strategies for homology detection in the 'twilight zone' where standard methods falter.
Main Methods:
- Review of customized sequence-based search tools for ncRNA applications.
- Focus on semi-global alignments and fragmented pattern search methods.
- Integration of fragmented sequence pattern search with secondary structure pattern search algorithms.
Main Results:
- Semi-global alignments and fragmented pattern search have significantly advanced ncRNA homology detection.
- Current research focuses on combining fragmented sequence and secondary structure pattern searches.
- Strategies are being developed to address challenges in the 'twilight zone' of sequence similarity.
Conclusions:
- Advanced computational approaches are crucial for effective ncRNA identification.
- Integrating sequence and structure information improves search sensitivity for difficult ncRNA families.
- Future developments aim to enhance homology searches in low-similarity regions.
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