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Author Topic: Opinion about the DSSR performance compared with the new "CompAnnotate".  (Read 1358 times)

Offline martingb

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Hello Dr. Xiang-Jun Lu:

This is the paper thas DSSR appears: https://academic.oup.com/nar/article/45/14/e136/3875524

I'd like to know your opinion about the DSSR performance compared with the new "CompAnnotate".

Regards. See you!
« Last Edit: April 10, 2018, 03:56:29 pm by martingb »

Offline xiangjun

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Ths link you gave is invalid. Could you fix it?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline martingb

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Done!

Offline xiangjun

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Thanks for posting a DSSR-related question on the 3DNA Forum, and for correcting the link to the CompAnnotate paper. I became aware of this work shortly after its publication, and believe it is a useful resource in RNA structural bioinformatics.

As a meta-analysis tool, CompAnnotate takes advantage of other tools (including DSSR) in the initial identification of base-pairs, as noted below:

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"Annotated base-pairing lists from the existing methods (MC-Annotate, RNAView, FR3D, DSSR and ClaRNA) are used as input for CompAnnotate and the corresponding modified base-pairing lists come as output."

To better appreciate the difference between DSSR and CompAnnotate, take a look of another tool "WebSTAR3D: a web server for RNA 3D structural alignment" developed by the same group. In the WebSTAR3D paper, the authors wrote:

Quote
Before aligning structures, STAR3D preprocesses PDB files with base-pairing annotation using either MC-Annotate (Gendron et al., 2001; Lemieux and Major, 2002) (for PDB inputs) or DSSR (Lu et al., 2015) (for PDB and mmCIF inputs) and pseudo-knot removal using RemovePseudoknots (Smit et al., 2008).

It is worth noting the following update on the WebSTAR3D website (see the attached screenshot),

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Update 7/11/2017: WebSTAR3D no longer employs MC-Annotate for base pairing annotation.

Further down the webpage, it is noted "Before aligning structures, WebSTAR3D preprocesses PDBs with base pairing annotation using DSSR". So now DSSR is the only choice left for base-pair annotation.

As documented in the User Manual, DSSR has many more features to offer than just identifying and annotating base pairs. In case users have any questions, the 3DNA Forum is the way to go.

Hope this clarifies some of your confusions.

Xiang-Jun
« Last Edit: April 10, 2018, 04:37:05 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline martingb

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Thanks you Dr.!

I didn't know that update on WebStar3D site

Regards!

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.