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R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N - Nucleic Acids Res. (2015)

Bottom Line: Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range.The output can be filtered and sorted in the browser.Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.

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Related in: MedlinePlus

The first two sections of the HTML output page, showing the Query Information component, including the alignment download option and the 3D viewer, and the Sequence Summary component. The first sequence in the Sequence Summary is highlighted in green because it is identical to the sequence in the reference 3D structure.
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Figure 4: The first two sections of the HTML output page, showing the Query Information component, including the alignment download option and the 3D viewer, and the Sequence Summary component. The first sequence in the Sequence Summary is highlighted in green because it is identical to the sequence in the reference 3D structure.

Mentions: Human-readable HTML output can be obtained from the server either by entering the desired nucleotide ranges manually on the input page or by providing the URL that encodes the search. The output web page contains three major components: (i) the ‘Query Information’ component, a summary of the query, (ii) a ‘Sequence Summary’ table listing the distinct sequence variants found in the alignment and (iii) a ‘Sequence Details’ table providing information for each sequence returned and its biological source. Figures 4 and 5 present a portion of the results from the sample query in Figure 3.


R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N - Nucleic Acids Res. (2015)

The first two sections of the HTML output page, showing the Query Information component, including the alignment download option and the 3D viewer, and the Sequence Summary component. The first sequence in the Sequence Summary is highlighted in green because it is identical to the sequence in the reference 3D structure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489222&req=5

Figure 4: The first two sections of the HTML output page, showing the Query Information component, including the alignment download option and the 3D viewer, and the Sequence Summary component. The first sequence in the Sequence Summary is highlighted in green because it is identical to the sequence in the reference 3D structure.
Mentions: Human-readable HTML output can be obtained from the server either by entering the desired nucleotide ranges manually on the input page or by providing the URL that encodes the search. The output web page contains three major components: (i) the ‘Query Information’ component, a summary of the query, (ii) a ‘Sequence Summary’ table listing the distinct sequence variants found in the alignment and (iii) a ‘Sequence Details’ table providing information for each sequence returned and its biological source. Figures 4 and 5 present a portion of the results from the sample query in Figure 3.

Bottom Line: Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range.The output can be filtered and sorted in the browser.Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.

Show MeSH
Related in: MedlinePlus