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RNApromo specifications

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Unique identifier OMICS_08118
Name RNApromo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for RNApromo

RNApromo citations

 (7)
library_books

Revealing protein–lncRNA interaction

2015
Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] []. a more extensive review of the influence of rna structural constraints 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 […]

library_books

High throughput characterization of protein–RNA interactions

2014
Brief Funct Genomics
PMCID: 4303715
PMID: 25504152
DOI: 10.1093/bfgp/elu047

[…] on the rbpmotif web server []., the second approach considers rna secondary structure explicitly and includes stochastic context-free grammar (scfg) and graphical approaches. cmfinder [] and rnapromo [] both start with a set of structures predicted using thermodynamic methods. rnapromo was used to predict motifs in sets of rnas bound by rbps in yeast []. maticzka and colleagues developed […]

library_books

Finding the target sites of RNA binding proteins

2013
PMCID: 4253089
PMID: 24217996
DOI: 10.1002/wrna.1201

[…] with preferred secondary structure contexts (e.g., memeris and rnacontext) and directly modeling secondary structure recognized by the rbp using stochastic context-free grammars (e.g., cmfinder and rnapromo). the former better reconstruct known binding preferences for sequence-specific rbps but are not suitable for modeling rbps that recognize shape and geometry of rnas. future work in rbp […]

library_books

The Drosophila RNA binding protein HOW controls the stability of dgrasp mRNA in the follicular epithelium

2013
Nucleic Acids Res
PMCID: 3919595
PMID: 24217913
DOI: 10.1093/nar/gkt1118

[…] d. mojavensis 5467–5542 nt; d. grimshawi 5399–5470 nt. sequence interval numbering is with respect to the translational start site (atg)., for prediction of rna structures, we used the ‘segal tool’ rnapromo (http://genie.weizmann.ac.il/pubs/rnamotifs08/rnamotifs08_predict.html). this tool predicts a structural motif common to a set of given rna sequences. the folding algorithm used in the segal […]

library_books

Classification and assessment tools for structural motif discovery algorithms

2013
BMC Bioinformatics
PMCID: 3698030
PMID: 23902564
DOI: 10.1186/1471-2105-14-S9-S4

[…] twice: first, to refine the initial alignment. second, to scan each sequence looking for hits, where top hits are treated as candidates. finally, motifs are merged to produce the final result., rnapromo [] is another em-based method for identifying rna motifs. it starts with a set of rna sequences and a set of suggested secondary structures. the motif prediction algorithm is composed of two […]

library_books

Computational identification of new structured cis regulatory elements in the 3′ untranslated region of human protein coding genes

2012
Nucleic Acids Res
PMCID: 3467077
PMID: 22821558
DOI: 10.1093/nar/gks684

[…] intensive., a number of programs have been applied to genome-wide identification of novel structured rnas (,), such as rnaz (), rna sampler (), evofold (), rsmatch (), foldalign (), cmfinder (), rnapromo () and locarna (). given the complexity and variety of structured rnas in a genome, the performance of different approaches differs considerably (,,). few studies have incorporated […]


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RNApromo institution(s)
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehoboth, Rehovot, Israel

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