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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F13%3A00067649%21RIV14-MSM-14740___
rdf:type
n5:Vysledek skos:Concept
dcterms:description
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. 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.
dcterms:title
RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi) RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
skos:prefLabel
RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi) RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
skos:notation
RIV/00216224:14740/13:00067649!RIV14-MSM-14740___
n5:predkladatel
n19:orjk%3A14740
n3:aktivita
n17:I n17:P
n3:aktivity
I, P(ED1.1.00/02.0068), P(GAP506/12/0038)
n3:cisloPeriodika
2
n3:dodaniDat
n4:2014
n3:domaciTvurceVysledku
n18:9031510
n3:druhVysledku
n13:J
n3:duvernostUdaju
n20:S
n3:entitaPredkladatele
n16:predkladatel
n3:idSjednocenehoVysledku
103125
n3:idVysledku
RIV/00216224:14740/13:00067649
n3:jazykVysledku
n14:eng
n3:klicovaSlova
2D structure; 2D mask; alignment; fungal phylogeny; 18 S rRNA; 28 S rRNA
n3:klicoveSlovo
n7:18%20S%20rRNA n7:alignment n7:28%20S%20rRNA n7:2D%20mask n7:2D%20structure n7:fungal%20phylogeny
n3:kodStatuVydavatele
DE - Spolková republika Německo
n3:kontrolniKodProRIV
[C170FA6FBF46]
n3:nazevZdroje
Mycological Progress
n3:obor
n15:CE
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
2
n3:projekt
n6:ED1.1.00%2F02.0068 n6:GAP506%2F12%2F0038
n3:rokUplatneniVysledku
n4:2013
n3:svazekPeriodika
12
n3:tvurceVysledku
Réblová, Kamila Réblová, Martina
n3:wos
000318044400012
s:issn
1617-416X
s:numberOfPages
15
n8:doi
10.1007/s11557-012-0836-8
n10:organizacniJednotka
14740