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:
"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:
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),
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
Topic: Opinion about the DSSR performance compared with the new "CompAnnotate". (Read 21099 times)