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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 citations

 (13)
library_books

Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection

2017
Sci Rep
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 RGKTSA […]

library_books

Transcription factor clusters regulate genes in eukaryotic cells

2017
eLife
PMCID: 5602325
PMID: 28841133
DOI: 10.7554/eLife.27451.030

[…] d 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 databas […]

library_books

In vitro evolution of distinct self cleaving ribozymes in diverse environments

2015
Nucleic Acids Res
PMCID: 4538833
PMID: 26130717
DOI: 10.1093/nar/gkv648

[…] able region of individual families. Conserved secondary structure predictions and sequence conservation between families were used to generate motif descriptors (Supplementary Figure S4) for use with RNABOB. The motif descriptors were used to determine the number and distribution of conserved motifs within the various populations. We used control data sets to estimate the false positive rates, whi […]

library_books

Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

2014
PLoS Genet
PMCID: 4133162
PMID: 25121733
DOI: 10.1371/journal.pgen.1004496

[…] d with (I) BLAST (v.2.2.25) with an E-value<10−4 (II) with infernal using covariance models from RFAM and (III) by hand as indicated in main text. Genes discovered in the reads only were found with rnabob in combination with various programs of the RNAViennaPackage v.2.0.2 (http://www.tbi.univie.ac.at/~ivo/RNA/). All ncRNA genes are available at the supplemental material in gff and fasta format […]

library_books

Next generation sequencing reveals how RNA catalysts evolve from random space

2013
Nucleic Acids Res
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, Supplem […]

library_books

Computational Small RNA Prediction in Bacteria

2013
Bioinform Biol Insights
PMCID: 3596055
PMID: 23516022
DOI: 10.4137/BBI.S11213

[…] quence 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 ana […]

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

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