RNABOB specifications

Information


Unique identifier OMICS_08373
Name RNABOB
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for RNABOB

RNABOB in publications

 (11)
PMCID: 5240108
PMID: 28094291
DOI: 10.1038/srep40599

[…] we performed genome-wide in silico analysis of consensus retinoic acid response element (rare) and vitamin d response element (vdre) motifs in the proximity of protein-coding genes using rnabob. the screening window was limited to the regions ±10 kb from transcription start sites and gene ends, according to previous studies. as target rare motif, we used the recurrent dr5 motif […]

PMCID: 5602325
PMID: 28841133
DOI: 10.7554/eLife.27451.030

[…] on 14 promoter sequences () using the iupac nucleotide code. the entire s. cerevisiae s288c genome was scanned in order to find all sequences that matched the pattern. the scanning was performed by rnabob software (), and collated for any further analysis and identification of the sequences lying within promoter regions. all information regarding s. cerevisiae genes was obtained from sgd […]

PMCID: 4538833
PMID: 26130717
DOI: 10.1093/nar/gkv648

[…] of 10 used to define sequence families., variation within families and shared features between families were both exploited to infer functional motifs using tallymer (), mafft () rnaalifold (), and rnabob (43). tallymer was used to identify common k-mers within a representative set of sequences from each population (representative sequences included only the most abundant sequence read […]

PMCID: 3902939
PMID: 24157838
DOI: 10.1093/nar/gkt949

[…] because functional rnas are generally more conserved in structure than sequence, we studied the conservation and evolution of specific structural elements of the typical dase ribozymes using rnabob, a structure-based search tool (). as indicated above, in the 49mer dase ribozyme, the bulge regions are critical for catalysis (). applying a general descriptor (supplementary text s4, […]

PMCID: 3596055
PMID: 23516022
DOI: 10.4137/BBI.S11213

[…] or structures. the secondary structure of srna, virtually represented in the form of a rna descriptor, can be scanned against the entire genome sequence using rnamotif, inclusive of rnamot and rnabob, or specific scripts written in palingol. the rna structure similarity and comparative genomics are routinely employed to identify srnas in most sequenced bacterial genomes. the comparative […]


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RNABOB institution(s)
University of California, Department of Chemistry, Irvine, CA, USA

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