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Miscellaneous items => FAQs => Topic started by: xiangjun on March 20, 2012, 02:35:25 pm

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Title: How to build a single-stranded RNA structure of arbitrary sequence?
Post by: xiangjun on March 20, 2012, 02:35:25 pm

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.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University