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 in publications

 (16)
PMCID: 5435971
PMID: 28158755
DOI: 10.1093/nar/gkx045

[…] sequence, we predict the 2d structure using programs such as mfold (), rnafold () and mc-fold (), or extract 2d information from known 3d structures using programs such as rnaview (), fr3d (), and mc-annotate (). a 2d rna graph is then built using the rules shown in . then, we use our data-mining prediction program called rnajag (rna-junction-as-graphs) to predict junction topologies based […]

PMCID: 4557229
PMID: 26329823
DOI: 10.1186/s12859-015-0718-6

[…] found in rna structural motifs., access to information about non-canonical interactions and multi-pairings is easier when the secondary structure is derived from atom coordinates. rnaview [], mc-annotate [], 3dna/dssr [] and our recently published rnapdbee [] are tools used for identifying and classifying rna base pairs, on structural data encoded in pdb files. all of these programs […]

PMCID: 4615831
PMID: 25932908
DOI: 10.1080/15476286.2015.1040977

[…] the final set included 198 domains (supplementary file s1). the “all rna” was extracted from kligun et al., 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 […]

PMCID: 4027170
PMID: 24623815
DOI: 10.1093/nar/gku191

[…] 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 […]

PMCID: 3905863
PMID: 24005040
DOI: 10.1093/nar/gkt795

[…] bn models for modules. given a pdb file, the coordinates of a particular module and an alignment, rmbuild analyses the pdb sequence and generates a bn model for the region of interest. rmbuild uses mc-annotate (), which identifies amongst other things all base pairs/triples and interacting structural elements. these features are modeled in the bn. as we already have the concrete fr3d module […]


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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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