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Author Topic: FRABASE  (Read 186 times)

Offline lvelve0901

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FRABASE
« on: October 18, 2017, 11:35:30 am »
Hi Xiangjun,

Do you have any idea that how different between DSSR and some online RNA database such as FRABASE in terms of secondary structure identification.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-231

Thanks.

Best,
Honglue

Offline xiangjun

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Re: FRABASE
« Reply #1 on: October 18, 2017, 01:00:29 pm »
Hi Honglue,

Please see the FAQ entry "How does DSSR compare with other tools?" in the DSSR User Manual for my thought on such comparisons.

In addition to the above general response, below is a quote from "RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures":

Quote
Several dedicated programs, web-accessible servers and databases have been proposed for processing and analysis of the PDB files (c.f. [3]) to study three-dimensional RNA structure. Among them, two particular programs are of general use and of specific importance to our work: 3DNA [4] and RNAView [5]. The first program calculates a complete set of rigid-body parameters that describe the detailed geometry of double helices extracted from the tertiary RNA structures. The second one finds all base pairs and multiplets in the RNA structure and offers the classification of canonical and non-canonical base-pairs. Both programs have been implemented in web-servers [2, 6].

In the current context, it is safe to say: DSSR = 3DNA + RNAview + ...

Xiang-Jun
« Last Edit: October 19, 2017, 01:45:49 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: FRABASE
« Reply #2 on: November 13, 2017, 10:06:40 am »
I see.

Thanks.

Best,
Honglue

 

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.