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Updated: Jul 10, 2026
11:04
RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
Published on: May 19, 2019
How accurately is ncRNA aligned within whole-genome multiple alignments?
Adrienne X Wang1, Walter L Ruzzo, Martin Tompa
1Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA. axwang@cs.washington.edu
BMC Bioinformatics
|October 30, 2007
Summary
Evaluating whole-genome multiple alignments in noncoding DNA reveals inaccuracies. While MULTIZ performs well, specific regions show potential for improved accuracy in evolutionary and genomic studies.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Multiple sequence alignment of homologous DNA is crucial for understanding evolutionary processes.
- The accuracy of whole-genome multiple alignments, especially in noncoding DNA, remains largely unevaluated.
Purpose of the Study:
- To assess the alignment accuracy of specific noncoding genomic regions.
- To identify areas within existing multiple alignments that could be improved.
Main Methods:
- Utilized noncoding RNA alignments from the Rfam database as a reference standard.
- Examined the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for human sequences.
- Identified instances of chimeric and partial alignments to human noncoding RNA elements.
Main Results:
- Discovered 638 instances of chimeric and partial alignments to human noncoding RNA elements.
- Determined that at least 225 of these alignments could be improved using simple methods.
- Predicted novel instances of known non-coding RNA families as a secondary outcome.
Conclusions:
- The MULTIZ alignment demonstrates reasonable accuracy in challenging noncoding genomic regions.
- Further improvements in alignment accuracy are possible for certain regions, enhancing evolutionary and genomic analyses.
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