RÉBLOVÁ, Martina a Kamila RÉBLOVÁ. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi). Mycological Progress. Heidelberg: Springer Heidelberg, 2013, roč. 12, č. 2, s. 305-319. ISSN 1617-416X. Dostupné z: https://dx.doi.org/10.1007/s11557-012-0836-8.
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Základní údaje
Originální název RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
Název česky RNA sekundární struktury, důležitý bioinformatický nástroj pro posílení více sekvencí: případová studie (Sordariomycetes, Fungi)
Autoři RÉBLOVÁ, Martina (203 Česká republika) a Kamila RÉBLOVÁ (203 Česká republika, garant, domácí).
Vydání Mycological Progress, Heidelberg, Springer Heidelberg, 2013, 1617-416X.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10600 1.6 Biological sciences
Stát vydavatele Německo
Utajení není předmětem státního či obchodního tajemství
Impakt faktor Impact factor: 1.543
Kód RIV RIV/00216224:14740/13:00067649
Organizační jednotka Středoevropský technologický institut
Doi http://dx.doi.org/10.1007/s11557-012-0836-8
UT WoS 000318044400012
Klíčová slova anglicky 2D structure; 2D mask; alignment; fungal phylogeny; 18 S rRNA; 28 S rRNA
Štítky ok, rivok
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: Olga Křížová, učo 56639. Změněno: 13. 2. 2014 11:53.
Anotace
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.
Návaznosti
ED1.1.00/02.0068, projekt VaVNázev: CEITEC - central european institute of technology
VytisknoutZobrazeno: 27. 4. 2024 04:49