Profiling and Searching for RNA Pseudoknot Structures in Genomes

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We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the al...

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Detalles Bibliográficos
Autores principales: Liu, Chunmei, Song, Yinglei, Malmberg, Russell L., Cai, Liming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2005
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120494/
http://dx.doi.org/10.1007/11567752_2
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author Liu, Chunmei
Song, Yinglei
Malmberg, Russell L.
Cai, Liming
author_facet Liu, Chunmei
Song, Yinglei
Malmberg, Russell L.
Cai, Liming
author_sort Liu, Chunmei
collection PubMed
description We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for structures that contain pseudoknot in genomes of a variety of organisms.
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spelling pubmed-71204942020-04-06 Profiling and Searching for RNA Pseudoknot Structures in Genomes Liu, Chunmei Song, Yinglei Malmberg, Russell L. Cai, Liming Transactions on Computational Systems Biology II Article We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for structures that contain pseudoknot in genomes of a variety of organisms. 2005 /pmc/articles/PMC7120494/ http://dx.doi.org/10.1007/11567752_2 Text en © Springer-Verlag Berlin Heidelberg 2005 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
Liu, Chunmei
Song, Yinglei
Malmberg, Russell L.
Cai, Liming
Profiling and Searching for RNA Pseudoknot Structures in Genomes
title Profiling and Searching for RNA Pseudoknot Structures in Genomes
title_full Profiling and Searching for RNA Pseudoknot Structures in Genomes
title_fullStr Profiling and Searching for RNA Pseudoknot Structures in Genomes
title_full_unstemmed Profiling and Searching for RNA Pseudoknot Structures in Genomes
title_short Profiling and Searching for RNA Pseudoknot Structures in Genomes
title_sort profiling and searching for rna pseudoknot structures in genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120494/
http://dx.doi.org/10.1007/11567752_2
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