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RNApromo specifications


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 in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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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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