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Mc-Annotate specifications

Information


Unique identifier OMICS_05577
Name Mc-Annotate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_05577
Name Mc-Annotate
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Mc-Annotate

Mc-Annotate citations

 (19)
call_split

CompAnnotate: a comparative approach to annotate base pairing interactions in RNA 3D structures

2017
Nucleic Acids Res
PMCID: 5737500
PMID: 28641399
DOI: 10.1093/nar/gkx538
call_split See protocol

[…] e (result improvements for sequence alignment are shown in ). With the support of input alignment, CompAnnotate does further aligning of base pairs considering the annotations from the existing tool (MC-Annotate, RNAView, FR3D, DSSR or ClaRNA). For each base pair of one RNA, a compatible base pair in the other RNA is searched, using the base correspondence as a guide. The resulting fine-tuned alig […]

call_split

Using sequence signatures and kink turn motifs in knowledge based statistical potentials for RNA structure prediction

2017
Nucleic Acids Res
PMCID: 5435971
PMID: 28158755
DOI: 10.1093/nar/gkx045
call_split See protocol

[…] The initial tree graph is generated based on the 2D structure information given in BPSEQ format. To generate 2D structures, we use available tools such as RNAView (), FR3D () and MC-Annotate () based on known 3D structures. We also tested our approach by predicting 2D structures by RNAfold () based on the dynamic programming algorithm proposed by Nussinov (,). We translate the […]

call_split

New in silico approach to assessing RNA secondary structures with non canonical base pairs

2015
BMC Bioinformatics
PMCID: 4557229
PMID: 26329823
DOI: 10.1186/s12859-015-0718-6
call_split See protocol

[…] NApdbee webserver []. At the input, RNApdbee accepts RNA atom coordinate data encoded in a PDB file. Next, it identifies base pairs using incorporated procedures of standalone versions of RNAView [], MC-Annotate [] or 3DNA/DSSR [], on user selection. Additional functions drive classification of non-canonical base pairs according to LW [, ] and Saenger [] nomenclatures, and identify pseudoknot orde […]

library_books

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

2015
BMC Bioinformatics
PMCID: 4464220
PMID: 26051557
DOI: 10.1186/1471-2105-16-S9-S6

[…] etermining the stacking base pairs are: 1) the ellipsoidal distance Djk<2.5, and Dkj<2.5;2) |zjk| and |zkj|<2Å;3 ) xjk2+yjk2<5Å and xkj2+ykj2<5Å. This procedure yields similar results compared to the MC-annotate software [] and was shown to be useful for characterizing both structural and dynamical properties of RNA molecules []. The software used to perform this structural analysis is available o […]

library_books

The role of RNA conformation in RNA protein recognition

2015
RNA Biol
PMCID: 4615831
PMID: 25932908
DOI: 10.1080/15476286.2015.1040977

[…] Characterizing the structural properties of RNA within the interfaces was conducted by MC-annotate program. The features were extracted as described in using an in–house Perl script converting the MC-annotate output files into binary format, i.e., each nucleotide was given a score of “1 […]

library_books

The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures

2014
Nucleic Acids Res
PMCID: 4027170
PMID: 24623815
DOI: 10.1093/nar/gku191

[…] act of contacts (frequency multiplied by the area size) for each bin. To compare our results with established approaches, for the same set of RNA structures we identified base–base interactions using MC-Annotate, a widely used RNA annotation method (). MC-Annotate detects and annotates base–base interactions using a procedure involving both geometric and probabilistic considerations (,). Figure s […]

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Mc-Annotate institution(s)
Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, CP, Succ Centre-Ville, Montréal, Québec, Canada
Mc-Annotate funding source(s)
This work was supported by a grant from the Canadian Institutes of Health Research (CIHR) (MT-14604) and a PhD scholarship from the CIHR, an MSc scholarship from the Fonds pour la formation de Chercheurs et l'Aide à la Recherche du Québec.

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