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Improbizer specifications

Information


Unique identifier OMICS_08102
Name Improbizer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_08102
Name Improbizer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Improbizer

Improbizer citations

 (20)
library_books

Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR mediated transcriptional regulation

2018
BMC Genomics
PMCID: 5784534
PMID: 29370758
DOI: 10.1186/s12864-018-4481-8

[…] To find conserved DNA sequence motifs in the C. diphtheriae NCTC 13129 genome, the motif-finding software Improbizer [] and the visualization program WebLogo 3 [] were used. Depending on the assumed motif location different input sequences were used. For the identification of σA promoter motifs the DNA se […]

library_books

RNAseq analysis of α proteobacterium Gluconobacter oxydans 621H

2018
BMC Genomics
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] 0 nt long sequence upstream of the translation start codon. Sequences with an accumulation of purines (>55%) were extracted. The extracted sequences were used to search for a conserved RBS motif with Improbizer []. Resulting data were visualized with Origin (OriginLab) and WebLogo []. […]

library_books

Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA seq technology

2017
BMC Genomics
PMCID: 5670726
PMID: 29100491
DOI: 10.1186/s12864-017-4235-z

[…] Similarly to the analysis of the promoter motifs, the Improbizer software [] was used to determine the consensus sequence of RBS and TLS in the sequence 50 base pairs upstream of the translation start codon of genes associated to the 1269 previously iden […]

library_books

Genome wide transcription start site profiling in biofilm grown Burkholderia cenocepacia J2315

2015
BMC Genomics
PMCID: 4603805
PMID: 26462475
DOI: 10.1186/s12864-015-1993-3

[…] using a custom background gene list consisting of all genes with an assigned pTSS. Alternative start codons were predicted using Prodigal []. DNA sequence motifs upstream of pTSS were identified with Improbizer [] using default parameters and motifs were then searched for in sequences upstream TSS belonging to other categories with Motif Matcher []; both programs consider location of the motif. Im […]

call_split

Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA sequencing provides detailed insights into its previously uncharted transcriptional landscape

2015
BMC Genomics
PMCID: 4342826
PMID: 25758049
DOI: 10.1186/s12864-015-1239-4
call_split See protocol

[…] To identify conserved sequence motifs for translation starts, ribosome binding sites and promoter regions of B. methanolicus MGA3, the motif-finding program Improbizer [] and the visualization tool WebLogo [] were used with default settings. The input differed according to the respective analysis context: For the determination of TLSs and promoter motifs […]

library_books

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

2014
PLoS Genet
PMCID: 3894158
PMID: 24453981
DOI: 10.1371/journal.pgen.1004008

[…] reciprocal BLASTing of each sequence against each other sequence within the alignment, and with three online motif search programs: Bioprospector (http://robotics.stanford.edu/~xsliu/BioProspector/), Improbizer(http://users.soe.ucsc.edu/~kent/improbizer/improbizer.html), and PhyloGibbs(http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl). GC contents were plotted using the crude alignments and G […]

Citations

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Improbizer institution(s)
Huntsman Cancer Institute, University of Utah, Circle of Hope, Salt Lake City, UT, USA; Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA

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