Detailed Information on Publication Record
2013
RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
RÉBLOVÁ, Martina and Kamila RÉBLOVÁBasic information
Original name
RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
Name in Czech
RNA sekundární struktury, důležitý bioinformatický nástroj pro posílení více sekvencí: případová studie (Sordariomycetes, Fungi)
Authors
RÉBLOVÁ, Martina (203 Czech Republic) and Kamila RÉBLOVÁ (203 Czech Republic, guarantor, belonging to the institution)
Edition
Mycological Progress, Heidelberg, Springer Heidelberg, 2013, 1617-416X
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10600 1.6 Biological sciences
Country of publisher
Germany
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 1.543
RIV identification code
RIV/00216224:14740/13:00067649
Organization unit
Central European Institute of Technology
UT WoS
000318044400012
Keywords in English
2D structure; 2D mask; alignment; fungal phylogeny; 18 S rRNA; 28 S rRNA
Tags
International impact, Reviewed
Změněno: 13/2/2014 11:53, Olga Křížová
Abstract
V originále
In a case study of fungi of the class Sordariomycetes, we evaluated the effect of multiple sequence alignment (MSA) on the reliability of the phylogenetic trees, topology and confidence of major phylogenetic clades. We compared two main approaches for constructing MSA based on (1) the knowledge of the secondary (2D) structure of ribosomal RNA (rRNA) genes, and automatic construction of MSA by four alignment programs characterized by different algorithms and evaluation methods, CLUSTAL, MAFFT, MUSCLE, and SAM. In the primary fungal sequences of the two functional rRNA genes, the nuclear small and large ribosomal subunits (18 S and 28 S), we identified four and six, respectively, highly variable regions, which correspond mainly to hairpin loops in the 2D structure. These loops are often positioned in expansion segments, which are missing or are not completely developed in the Archaeal and Eubacterial kingdoms. Proper sorting of these sites was a key for constructing an accurate MSA. We utilized DNA sequences from 28 S as an example for one-gene analysis. Five different MSAs were created and analyzed with maximum parsimony and maximum likelihood methods. The phylogenies inferred from the alignments improved with 2D structure with identified homologous segments, and those constructed using the MAFFT alignment program, with all highly variable regions included, provided the most reliable phylograms with higher bootstrap support for the majority of clades. We illustrate and provide examples demonstrating that re-evaluating ambiguous positions in the consensus sequences using 2D structure and covariance is a promising means in order to improve the quality and reliability of sequence alignments.
Links
| ED1.1.00/02.0068, research and development project |
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