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RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency

The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary st...

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Detalles Bibliográficos
Autor principal: Wright, Erik S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161358/
https://www.ncbi.nlm.nih.gov/pubmed/32005745
http://dx.doi.org/10.1261/rna.073015.119
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author Wright, Erik S.
author_facet Wright, Erik S.
author_sort Wright, Erik S.
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description The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the observation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned. Overall, RNAconTest provides a means of testing and improving tools for comparative RNA analysis, as well as highlighting the best available approaches. RNAconTest is available from the DECIPHER website (http://DECIPHER.codes/Downloads.html).
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spelling pubmed-71613582021-05-01 RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency Wright, Erik S. RNA Bioinformatics The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the observation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned. Overall, RNAconTest provides a means of testing and improving tools for comparative RNA analysis, as well as highlighting the best available approaches. RNAconTest is available from the DECIPHER website (http://DECIPHER.codes/Downloads.html). Cold Spring Harbor Laboratory Press 2020-05 /pmc/articles/PMC7161358/ /pubmed/32005745 http://dx.doi.org/10.1261/rna.073015.119 Text en © 2020 Wright; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Bioinformatics
Wright, Erik S.
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title_full RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title_fullStr RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title_full_unstemmed RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title_short RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency
title_sort rnacontest: comparing tools for noncoding rna multiple sequence alignment based on structural consistency
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161358/
https://www.ncbi.nlm.nih.gov/pubmed/32005745
http://dx.doi.org/10.1261/rna.073015.119
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