Center for Molecular Biology of RNA

Web Servers

• tRNAscan-SE for tRNA predictions
• snoscan for C/D box snoRNA predictions
• snoGPS for H/ACA snoRNA predictions

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Databases

• UCSC Archaeal Genome Browser
• UCSC Microbial Genome Browser
• Genomic tRNA Database
• snoRNA Database for Yeast and Archaea

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Crystallography on OS X

Determining the crystal structure of RNA using OSX software.

• COOT

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Pymol plugins for axis and angle rotation

• Full details of Euler - Rodriguez Pymol plugin
• If you use this plug-in, please cite: Mohan, S., Donohue, J. P. & Noller, H. F. Molecular mechanics of 30S subunit head rotation. Proc. Natl. Acad. Sci. U. S. A. 111, 13325-13330.
  • Pymol plugin for Euler-Rodriguez Transformation calculation of axis and angle or rotation (…save as)
  • example use of Euler-Rodriguez plugin (…save as)
  • Details for Euler-Rodriguez Transformation calculation of axis and angle or rotation

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Pymol plugin for identifying domains

Pymol plugin for identifying domains (…save as)

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PDB to Restraints

Webserver for generating Stacking and Base Pair restraints from a PDB coordinate file.

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PDB to pymol base pair cones

Webserver for generating cone type basepairs for pymol.

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XRNA

Java program for creating, manipulating and annotating secondary structure graphics.

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XRNA2.0

(Beta) Webserver for creating, manipulating and annotating secondary structure graphics. It can handle pseudoknots, multiple chains, insertions, deletions

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Intronerator

A set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans.

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Ares lab Yeast Intron Database

Web database lookup tools.

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Experimental Design and Optimization

Web interface for experimental design and optimization tools.

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Sequence Logo Generator

Sequence Logo Generator, from PSWM or PSSM .

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