RNA secondary structure, an important bioinformatics tool to
enhance multiple sequence alignment: a case study
(Sordariomycetes, Fungi)

J 2013

RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

RÉBLOVÁ, Martina a Kamila RÉBLOVÁ

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

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

Změněno: 13. 2. 2014 11:53, Olga Křížová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

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.

@article{1083000,
   author = {Réblová, Martina and Réblová, Kamila},
   article_location = {Heidelberg},
   article_number = {2},
   doi = {http://dx.doi.org/10.1007/s11557-012-0836-8},
   keywords = {2D structure; 2D mask; alignment; fungal phylogeny; 18 S rRNA; 28 S rRNA},
   language = {eng},
   issn = {1617-416X},
   journal = {Mycological Progress},
   title = {RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)},
   volume = {12},
   year = {2013}
}

TY  - JOUR
ID  - 1083000
AU  - Réblová, Martina - Réblová, Kamila
PY  - 2013
TI  - RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
JF  - Mycological Progress
VL  - 12
IS  - 2
SP  - 305-319
EP  - 305-319
PB  - Springer Heidelberg
SN  - 1617416X
KW  - 2D structure
KW  - 2D mask
KW  - alignment
KW  - fungal phylogeny
KW  - 18 S rRNA
KW  - 28 S rRNA
N2  - 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.
ER  -

RÉBLOVÁ, Martina a Kamila RÉBLOVÁ. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi). \textit{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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