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Protocols

BoBro specifications

Information


Unique identifier OMICS_19901
Name BoBro
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/bobro/BoBro2.0.tar.gz
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ying Xu

Additional information


BoBro is also included in DMINDA : http://bmbl.sdstate.edu/DMINDA2/download.php

Publications for BoBro

BoBro citations

 (5)
library_books

An integrative and applicable phylogenetic footprinting framework for cis regulatory motifs identification in prokaryotic genomes

2016
BMC Genomics
PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] We compared the prediction of MP3 with six de novo motif finding tools: BOBRO, MDscan, Bioprospector, MEME, CONSENSUS, CUBIC, and MicroFootprinter. MicroFootprinter is designed for phylogenetic footprinting on prokaryotic genomes and can generate orthologous promoters on […]

library_books

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

2016
Sci Rep
PMCID: 4792141
PMID: 26975728
DOI: 10.1038/srep23030

[…] We ran our in-house motif-finding tool, BOBRO, on the orthologous promoter set to find motifs. BOBRO had been tested on phylogenetic footprinting data and showed consistently better performance than other existing tools. The identified moti […]

library_books

Global O GlcNAc Levels Modulate Transcription of the Adipocyte Secretome during Chronic Insulin Resistance

2015
PMCID: 4302944
PMID: 25657638
DOI: 10.3389/fendo.2014.00223

[…] ere used as the negative set for human, mouse, and rat (). Seven motif finding tools were used for primary motif finding: AlignACE (), Bioprospecter (), CONSENSUS(), CUBIC (), MDscan (), MEME (), and BOBRO (). For each candidate, a position weight matrix and scoring matrix were generated (Table in Supplementary Material). Corresponding transcription factor binding motifs were determined by analyz […]

call_split

Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress

2013
Biotechnol Biofuels
PMCID: 3848806
PMID: 24028713
DOI: 10.1186/1754-6834-6-131
call_split See protocol

[…] Genes that were considered significantly differentially expressed by microarray were analyzed by BoBro and a motif analysis toolkit to identify potential cis regulatory motifs [,]. These putative motifs were evaluated by a phylogenetic footprinting framework utilizing 39 Clostridium genome sequen […]

library_books

Genome scale identification of cell wall related genes in Arabidopsis based on co expression network analysis

2012
BMC Plant Biol
PMCID: 3463447
PMID: 22877077
DOI: 10.1186/1471-2229-12-138

[…] dditional file : Figure S2a), providing a strong evidence that most genes in the same module are transcriptionally co-regulated. For the all motifs in each module, we also provided the p-values using BOBRO (Additional file : Table S2) [].Sequence comparison with known cis regulatory motifs in the PLACE and AGRIS databases reveal that 769 of the 1,329 motifs (58%) match well with 622 of the 1,009 a […]

Citations

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BoBro institution(s)
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA; School of Mathematics, Shandong University, Jinan, China; Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA; BioEnergy Science Center, Oak Ridge, TN, USA; College of Computer Science and Technology, Jilin University, Changchun, China
BoBro funding source(s)
Supported in part by National Science Foundation (NSF/MCB-0958172, NSF/DEB–0830024 and USG Inter-Institutional Collaborative Grant), by the U.S. Department of Energy’s BioEnergy Science Center (BESC) grant through the Office of Biological and Environmental Research, by grants 61070095, 60873207 and 61272016 from NSFC, and ZR2010FM014 from NSF of Shandong Province, China, by grants ZR2011FQ010 and ZR2010AQ018 from NSF of Shandong Province, China.

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