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postgraduate thesis: Efficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction

TitleEfficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction
Authors
Advisors
Advisor(s):Ting, HF
Issue Date2013
PublisherThe University of Hong Kong (Pokfulam, Hong Kong)
Citation
Li, Y. [李耀满]. (2013). Efficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5153733
AbstractRNA plays an important role in molecular biology. RNA sequence comparison is an important method to analysis the gene expression. Since aligning RNA reads needs to handle gaps, mutations, poly-A tails, etc. It is much more difficult than aligning other sequences. In this thesis, we study the RNA-Seq align tools, the existing gene information database and how to improve the accuracy of alignment and predict RNA secondary structure. The known gene information database contains a lot of reliable gene information that has been discovered. And we note most DNA align tools are well developed. They can run much faster than existing RNA-Seq align tools and have higher sensitivity and accuracy. Combining with the known gene information database, we present a method to align RNA-Seq data by using DNA align tools. I.e. we use the DNA align tools to do alignment and use the gene information to convert the alignment to genome based. The gene information database, though updated daily, there are still a lot of genes and alternative splicings that hadn't been discovered. If our RNA align tool only relies on the known gene database, then there may be a lot reads that come from unknown gene or alternative splicing cannot be aligned. Thus, we show a combinational method that can cover potential alternative splicing junction sites. Combining with the original gene database, the new align tools can cover most alignments which are reported by other RNA-Seq align tools. Recently a lot of RNA-Seq align tools have been developed. They are more powerful and faster than the old generation tools. However, the RNA read alignment is much more complicated than other sequence alignment. The alignments reported by some RNA-Seq align tools have low accuracy. We present a simple and efficient filter method based on the quality score of the reads. It can filter most low accuracy alignments. At last, we present a RNA secondary prediction method that can predict pseudoknot(a type of RNA secondary structure) with high sensitivity and specificity.
DegreeMaster of Philosophy
SubjectNucleotide sequence - Data processing
Dept/ProgramComputer Science
Persistent Identifierhttp://hdl.handle.net/10722/195977

 

DC FieldValueLanguage
dc.contributor.advisorTing, HF-
dc.contributor.authorLi, Yaoman-
dc.contributor.author李耀满-
dc.date.accessioned2014-03-21T03:50:02Z-
dc.date.available2014-03-21T03:50:02Z-
dc.date.issued2013-
dc.identifier.citationLi, Y. [李耀满]. (2013). Efficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5153733-
dc.identifier.urihttp://hdl.handle.net/10722/195977-
dc.description.abstractRNA plays an important role in molecular biology. RNA sequence comparison is an important method to analysis the gene expression. Since aligning RNA reads needs to handle gaps, mutations, poly-A tails, etc. It is much more difficult than aligning other sequences. In this thesis, we study the RNA-Seq align tools, the existing gene information database and how to improve the accuracy of alignment and predict RNA secondary structure. The known gene information database contains a lot of reliable gene information that has been discovered. And we note most DNA align tools are well developed. They can run much faster than existing RNA-Seq align tools and have higher sensitivity and accuracy. Combining with the known gene information database, we present a method to align RNA-Seq data by using DNA align tools. I.e. we use the DNA align tools to do alignment and use the gene information to convert the alignment to genome based. The gene information database, though updated daily, there are still a lot of genes and alternative splicings that hadn't been discovered. If our RNA align tool only relies on the known gene database, then there may be a lot reads that come from unknown gene or alternative splicing cannot be aligned. Thus, we show a combinational method that can cover potential alternative splicing junction sites. Combining with the original gene database, the new align tools can cover most alignments which are reported by other RNA-Seq align tools. Recently a lot of RNA-Seq align tools have been developed. They are more powerful and faster than the old generation tools. However, the RNA read alignment is much more complicated than other sequence alignment. The alignments reported by some RNA-Seq align tools have low accuracy. We present a simple and efficient filter method based on the quality score of the reads. It can filter most low accuracy alignments. At last, we present a RNA secondary prediction method that can predict pseudoknot(a type of RNA secondary structure) with high sensitivity and specificity.-
dc.languageeng-
dc.publisherThe University of Hong Kong (Pokfulam, Hong Kong)-
dc.relation.ispartofHKU Theses Online (HKUTO)-
dc.rightsThe author retains all proprietary rights, (such as patent rights) and the right to use in future works.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.lcshNucleotide sequence - Data processing-
dc.titleEfficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction-
dc.typePG_Thesis-
dc.identifier.hkulb5153733-
dc.description.thesisnameMaster of Philosophy-
dc.description.thesislevelMaster-
dc.description.thesisdisciplineComputer Science-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.5353/th_b5153733-

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