A statistical score for assessing the quality of multiple sequence alignments

Ahola, Virpi; Aittokallio, Tero; Vihinen, Mauno; Uusipaikka, Esa

doi:10.1186/1471-2105-7-484

Cited by 44 publications

(25 citation statements)

References 49 publications

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“…Full length bHLH protein sequences of the T. castaneum and one closest homologue from Drosophila melanogaster, Apis mellifera or Gallus gallus were aligned in MAFFT (Ahola et al, 2006) with the L-INS-i iterative refinement option on the MAFFT server (http://align.bmr.kyushu-u.ac.jp/mafft/online/server/). MAFFT with the L-INS-i option has shown to be the most accurate and consistent method for aligning protein sequences (Atlekar et al, 2004; Golubchik et al, 2007).…”

Section: Methodsmentioning

confidence: 99%

Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum

Bitra

Tan

Dowling

et al. 2009

Gene

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The basic helix-loop-helix transcription factors are present in animals, plants and fungi and play important roles in the control of cellular proliferation, tissue differentiation, development and detoxification. Although insect genomes contain more than 50 Helix-Loop-Helix transcription factors, the functions of only a few are known. RNAi has become a widely used tool to knockdown the expression to analyze the function of genes. As RNAi works well in Tribolium castaneum, we utilized this insect and RNAi to determine functions of 19 bHLH transcription factors belonging to PAS and HES families during the larval stages of the red flour beetle, T. castaneum. We searched the genome sequence of T. castaneum and identified 53 bHLH genes. Phylogenetic analyses classified these 53 genes into ten families; PAS, HES, Myc/USF, Hand, Mesp, Shout, p48, NeuroD/ Neurogenin, Atonal and AS-C. In RNAi studies, knocking-down the expression of seven members of the PAS and HES families affected the growth and development of T. castaneum. An inability to grow to reach critical weight to undergo metamorphosis, failure to complete larval-pupal or pupaladult ecdysis and abnormal wing development are among the most common phenotypes observed in RNAi insects. Among the bHLH transcription factors studied, the steroid receptor coactivator (SRC) showed the most severe phenotypes. Knock-down in the expression of the gene coding for SRC caused growth arrest by affecting the regulation of lipid metabolism. These studies demonstrate the power of RNAi for functional characterization of members of the multigene families in this model insect.

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Section: Methodsmentioning

confidence: 99%

Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum

Bitra

Tan

Dowling

et al. 2009

Gene

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“…MAFFT v6.603 [28] was used in the alignment employing L-INS-I, which is considered to be one of the most accurate MSA methods [29,30]. Maximum likelihood (ML) trees were built on the MSA datasets by using PhyML v2.4.4 [31].…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production

et al. 2009

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NAM, ATAF, and CUC2 (NAC) proteins are encoded by one of the largest plant-specific transcription factor gene families. The functions of many NAC proteins relate to different aspects of lignocellulosic biomass production, and a small group of NAC transcription factors has been characterized as master regulators of plant cell wall development. In the present study, a total of 1,232 NAC protein sequences from 11 different organisms were analyzed by sequence phylogeny based on protein DNA-binding domains. We included eight whole genomes (Arabidopsis, rice, poplar, grape, sorghum, soybean, moss (Physcomitrella patens), and spike moss (Selaginella moellendorffii)) and three not yet fully sequenced genomes (maize, switchgrass, and Medicago truncatula) in our analyses. Ninety-two potential PvNAC genes from switchgrass and 148 PtNAC genes from poplar were identified. The 1,232 NAC proteins were phylogenetically classified into eight subfamilies, each of which was further divided into subgroups according to their tree topology. The phylogenetic subgroups were then grouped into different clades each sharing conserved motif patterns in the C-terminal sequences, and those that may function in plant cell wall development were further identified through motif grouping and gene expression pattern analysis using publicly available microarray data. Our results provide a bioinformatic baseline for further functional analyses of candidate NAC genes for improving cell wall and environmental tolerance traits in the bioenergy crops switchgrass and poplar.

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“…Protein repeats were characterised using RADAR (Heger and Holm, 2000; http://www.ebi.ac.uk/Radar/). Protein sequences were aligned in MAFFT (Katoh et al, 2005) using the L-INS-i iterative refinement methodology (Ahola et al, 2006). Initial formatting of alignments was carried out in BOXSHADE (http:// www.ch.embnet.org/software/BOX_form.html) followed by manual coloration.…”

Section: Sequence Retrieval Alignment and Analysismentioning

confidence: 99%

Molecular phylogenetics of ascomycotal adhesins—A novel family of putative cell-surface adhesive proteins in fission yeasts

Linder¹,

Gustafsson²

2008

Fungal Genetics and Biology

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A statistical score for assessing the quality of multiple sequence alignments

Cited by 44 publications

References 49 publications

Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum

Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum

A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production

Molecular phylogenetics of ascomycotal adhesins—A novel family of putative cell-surface adhesive proteins in fission yeasts

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