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locarna tool  (Informatik Inc)

 
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    Informatik Inc locarna tool
    Locarna Tool, supplied by Informatik Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/locarna tool/product/Informatik Inc
    Average 90 stars, based on 1 article reviews
    locarna tool - by Bioz Stars, 2026-05
    90/100 stars

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    Conservation of Cas12a-associated repeat sequence and folding. A , nearest neighbor joining tree and ( B ) alignment of 28 type V CRISPR repeats. The <t>LocARNA-predicted</t> secondary structure ( right ) is indicated at the top of the sequence alignment. The 5′ leader sequence is highlighted in orange and the stem and loop of the predicted stem–loop structure is highlighted in green and blue , respectively. C , repeat consensus sequence shown with the secondary structure predicted for the alignment in ( A ) with the same color coding. D , superimposed image of the representative structures of the major cluster in the free pseudoknot ( magenta ) and AsCas12a-bound pseudoknot ( green ) in the AsCas12a RNP complex from 1 μs molecular dynamics simulation trajectories. RNP, ribonucleoprotein.
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    ITS2 sequence structure-based alignment generated by LocaRNA-P. Dot-bracket notation represents unpaired bases and matching parenthesized positions represent paired bases. The red regions indicate structure reliability, the yellow regions represent sequence reliability, and the thin line shows the combined column-reliability.

    Journal: Journal of Fungi

    Article Title: Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota)

    doi: 10.3390/jof9090894

    Figure Lengend Snippet: ITS2 sequence structure-based alignment generated by LocaRNA-P. Dot-bracket notation represents unpaired bases and matching parenthesized positions represent paired bases. The red regions indicate structure reliability, the yellow regions represent sequence reliability, and the thin line shows the combined column-reliability.

    Article Snippet: Then, these structures were input into LocARNA v2.0 ( https://rna.informatik.uni-freiburg.de/LocARNA/Input.jsp;jsessionid=115161C5C9E9AB44CC6D3C81763A1699 , accessed on 2 February 2022) [ ] software to perform structural-alignment and consensus secondary structure modelling—see .

    Techniques: Sequencing, Generated

    Conservation of Cas12a-associated repeat sequence and folding. A , nearest neighbor joining tree and ( B ) alignment of 28 type V CRISPR repeats. The LocARNA-predicted secondary structure ( right ) is indicated at the top of the sequence alignment. The 5′ leader sequence is highlighted in orange and the stem and loop of the predicted stem–loop structure is highlighted in green and blue , respectively. C , repeat consensus sequence shown with the secondary structure predicted for the alignment in ( A ) with the same color coding. D , superimposed image of the representative structures of the major cluster in the free pseudoknot ( magenta ) and AsCas12a-bound pseudoknot ( green ) in the AsCas12a RNP complex from 1 μs molecular dynamics simulation trajectories. RNP, ribonucleoprotein.

    Journal: The Journal of Biological Chemistry

    Article Title: Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly

    doi: 10.1016/j.jbc.2023.104700

    Figure Lengend Snippet: Conservation of Cas12a-associated repeat sequence and folding. A , nearest neighbor joining tree and ( B ) alignment of 28 type V CRISPR repeats. The LocARNA-predicted secondary structure ( right ) is indicated at the top of the sequence alignment. The 5′ leader sequence is highlighted in orange and the stem and loop of the predicted stem–loop structure is highlighted in green and blue , respectively. C , repeat consensus sequence shown with the secondary structure predicted for the alignment in ( A ) with the same color coding. D , superimposed image of the representative structures of the major cluster in the free pseudoknot ( magenta ) and AsCas12a-bound pseudoknot ( green ) in the AsCas12a RNP complex from 1 μs molecular dynamics simulation trajectories. RNP, ribonucleoprotein.

    Article Snippet: These repeats were aligned and their secondary structure predicted with LocARNA ( https://rna.informatik.uni-freiburg.de/LocARNA ) ( ).

    Techniques: Sequencing, CRISPR