RNAcontext specifications

Information


Unique identifier OMICS_02253
Name RNAcontext
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Information


Unique identifier OMICS_02253
Name RNAcontext
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RNAcontext

RNAcontext in publications

 (10)
PMCID: 5848454
PMID: 29529991
DOI: 10.1186/s12859-018-2091-8

[…] intensity for approximately 240,000 rna probe sequences. position frequency matrices were derived using top 10 probes for each experiment []. many previous methods including 1nn, deepbind, rck/rnacontext were all trained and tested on this dataset. we used the position frequency matrices in this dataset to form our training set, and the probes to form our in vitro testing set., […]

PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] binding sites on a genome-wide scale. fig. 2 , we firstly compare it with state-of-the-art method ionmf, which has shown better performance than other existing methods [], such as graphprot [] and rnacontext []. as shown in table , we can see that ideep outperform ionmf on most of the 31 experiments, the average auc of the 31 experiments increases from 0.85±0.08 of ionmf to 0.90±0.08 of ideep. […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] previously developed tools for dna and protein motif discoveries can be implemented to the rna datasets and performed well, which include homer, meme, cermit, glam2, matrixreduce, and rnacontext. although there are tools for the ncrna secondary structure prediction and functional annotation, such as graphprot, capr, and lncrna2function, there are still significant challenges […]

PMCID: 4894278
PMID: 26787667
DOI: 10.1093/bioinformatics/btw003

[…] parsimonious factor models. table 1.a critical distance diagram of average ranks is shown above., a critical distance diagram of average ranks is shown above., we compared ionmf with graphprot and rnacontext on the same dataset used by maticzka et al. (). ionmf performed best on 13 out of 24 rbp experiments (auc=0.907±0.041). critical difference diagrams show equivalent performance of ionmf […]

PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] in the context of motif discovery at rbp binding sites can be found in []. the already mentioned memeris [], cmfinder [], rnapromo [], structred [], the algorithm by li and collaborators [], rnacontext and rbpmotif [, ], graphprot [] and zagros [] are all tools that use, with different strategies and to different extent, secondary structure information to determine more specific binding […]


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RNAcontext institution(s)
Department of Computer Science, University of Toronto, Toronto, ON, Canada

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