Raccess specifications

Information


Unique identifier OMICS_16632
Name Raccess
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability No
Maintained No

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Publication for Raccess

Raccess in publications

 (11)
PMCID: 5686824
PMID: 29137642
DOI: 10.1186/s12934-017-0812-8

[…] centroidfold tool for the structure prediction []. based on a generalized centroid estimator, centroidfold is one of the most accurate tools for predicting rna secondary structures.then, we used the raccess algorithm [] to compute the accessibility of segment [a, b] = [x, x + l − 1] in the rna sequence for all the positions x with fixed length l (acc.len) = 5, 10. the thermodynamic energy […]

PMCID: 5617207
PMID: 28966976
DOI: 10.1523/ENEURO.0013-17.2017

[…] pclamp10 software (molecular devices, rrid:scr_011323). data were analyzed using clampfit (molecular devices) and custom procedures in igorpro (wavemetrics, rrid: scr_00325). only cells with an raccess below 15 mω were accepted. in current-clamp mode, neurons were subjected to hyperpolarizing and depolarizing step pulses (±40 pa). rna was collected at the end of recording (typically 3–5 min […]

PMCID: 5465533
PMID: 28595592
DOI: 10.1186/s13062-017-0183-4

[…] was implemented as a function of the tcc library in bioconductor []., we previously developed a series of computational pipelines including various computational tools for sequence analysis, such as raccess [], tantan [], last [, ], intarna [], and ractip [], for predicting human lncrna-rna interactions []. furthermore, all predicted human lncrna-rna interactions are available from our database […]

PMCID: 5378133
PMID: 28275121
DOI: 10.1098/rsif.2016.0999

[…] selection produced a model with similar variables and parameter estimates (a and ). the final model constructed with the forward-entry method included the electrophysiological variables ileak, raccess, ccell, kh, imax, rinput, transient current, ratio current, v2 h and tail current. in what follows, this model is used to predict islet cell type. table 3. figure 6. table 4., the model […]

PMCID: 5578739
PMID: 28762944
DOI: 10.7554/eLife.25462.023

[…] configuration with 6–8 mω pipettes filled with internal solution to which s-ampa (100 μm; tocris) was added. whole-cell recordings in organotypic slice cultures were made with 3–5 mω pipettes (raccess < 20 mω, and rinput > 10× raccess). during mepsc recordings, ttx (1 μm; tocris) and picrotoxin (100 μm; sigma) were added to the bath. where indicated, the following drugs were added […]


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Raccess institution(s)
Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, Chiba, Japan; INTEC Systems Institute, Inc., Biobusiness Division, Tokyo, Japan; Stelic Institute & Co., Tokyo, Japan; Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan; Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
Raccess funding source(s)
Supported by ‘Functional RNA Project’ funded by the New Energy and Industrial Technology Development Organization (NEDO), Japan; a Grant-in-Aid for Young Scientists (21700330); a Grant-in-Aid for Scientific Research (A) (22240031); grants from the Contract Development Program of Japan Science and Technology Agency.

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