RNAmine statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RNAmine

Tool usage distribution map

This map represents all the scientific publications referring to RNAmine per scientific context
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RNAmine specifications


Unique identifier OMICS_08117
Name RNAmine
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


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Publication for RNAmine

RNAmine citations


RNA motif discovery: a computational overview

Biol Direct
PMCID: 4600295
PMID: 26453353
DOI: 10.1186/s13062-015-0090-5

[…] As opposed to comRNA which uses several ad-hoc steps, RNAmine proposed in [] uses a more systematic approach using graph mining ideas to extract stem patterns. The subarea of graph mining [] is pretty mature within the area of frequent pattern mining. In […]


Classification and assessment tools for structural motif discovery algorithms

BMC Bioinformatics
PMCID: 3698030
PMID: 23902564
DOI: 10.1186/1471-2105-14-S9-S4

[…] very node is connected to every other node. After that, a graph technique similar to topological sort is applied to find the best assemblies of stems. Finally, the highest ranking motifs are reported.RNAmine [] uses graph mining algorithm to discover motifs shared by a subset of different RNA sequences. An RNA sequence and its secondary structure is represented as a directed labeled graph, called […]


Software.ncrna.org: web servers for analyses of RNA sequences

Nucleic Acids Res
PMCID: 2447773
PMID: 18440970
DOI: 10.1093/nar/gkn222

[…] y sequences to the template structure with annotations of the secondary structures and the same kind of figures of the structures as SCARNA.On the ‘structural motif extraction’ menu, users can select RNAmine, which accepts either direct input or uploading of a file of RNA sequences in multi-FASTA format. The server outputs the extracted motifs as abstract figures of the secondary structures and th […]


A fast structural multiple alignment method for long RNA sequences

BMC Bioinformatics
PMCID: 2375124
PMID: 18215258
DOI: 10.1186/1471-2105-9-33

[…] tifs without aligning the whole sequences. For structural motif finding, Yao et al. proposed an algorithm based on covariance models (CMfinder) [], and Hamada et al. proposed a graph mining approach (RNAmine) [].Here we propose a method, implemented in MXSCARNA, for fast multiple alignments of RNA sequences. This method extends our previous work in pairwise alignments (SCARNA) [] to progressive mu […]

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RNAmine institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan

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