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RNAlocopt specifications

Information


Unique identifier OMICS_16661
Name RNAlocopt
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Source code URL http://bioinformatics.bc.edu/clotelab/RNAlocopt/srcPLoSfinal16nov2010/SOFTWARE.tar.gz
Maintained Yes

Documentation


Maintainer


  • person_outline Peter Clote

Publication for RNAlocopt

RNAlocopt citations

 (2)
library_books

Random versus Deterministic Descent in RNA Energy Landscape Analysis

2016
Adv Bioinformatics
PMCID: 4808746
PMID: 27110241
DOI: 10.1155/2016/9654921

[…] bopt for such a task, where indeed the sets of local minima are identical to the current RNAsubopt plus Barriers results, is beyond the scope of the present paper.Lorenz and Clote introduce in [] the RNAlocopt tool for sampling and approximating the total number of metastable conformations using the partition function. However, currently the RNAlocopt tool has only been implemented by using the Tu […]

library_books

Asymptotic structural properties of quasi random saturated structures of RNA

2013
PMCID: 3818986
PMID: 24156624
DOI: 10.1186/1748-7188-8-24

[…] [,] could be extended to do so for both homopolymers and RNA sequences. (Note that the program RNAsat, described in [], can sample saturated structures in the Turner energy landscape, and the program RNAlocopt, described in [], can sample locally optimal structures in the Turner energy landscape). In contrast, it is extremely simple to implement a program to sample quasi-random saturated structure […]


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RNAlocopt institution(s)
Department of Mathematics and Computer Science, Denison University, Granville, OH, USA; Biology Department, Boston College, Chestnut Hill, MA, USA
RNAlocopt funding source(s)
This wok was supported by the National Science Foundation under grants DBI-0543506 and DMS-0817971 and by the form of a Chair of Excellence by the Digiteo Foundation.

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