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Author Topic: How to build a single-stranded RNA structure of arbitrary sequence?  (Read 2556 times)

Offline xiangjun

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As of v2.1, the fiber utility has several new options that make building single-stranded RNA structures of arbitrary sequence a snap:
  • -s for single-strand
  • -r for RNA structure
  • -seq for specifying arbitrary sequence directly on the command line
For example, to generate a single-stranded RNA structure of sequence 'AUUGGUUC', do the following:
Code: [Select]
fiber -s -r -seq=AUUGGUUC ss-RNA.pdb
# the -s and -r options can be combined as -sr or -rs
fiber -sr -seq=AUUGGUUC ss-RNA.pdb

Technically, the RNA model is based on A-DNA model (#1 in the list), with the O2' atom attached on the sugar, and T replaced by U. The -s option simply extracts the leading strand from the default duplex.
« Last Edit: March 20, 2012, 09:17:10 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.