Improbizer protocols

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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

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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 in pipeline

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

[…] 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. […]


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Improbizer in publications

 (30)
PMCID: 5784534
PMID: 29370758
DOI: 10.1186/s12864-018-4481-8

[…] []. newly identified genes were assigned with a locus tag containing a unique identifier., 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 […]

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

[…] primary operons, with tsss assigned to the first gene of an operon, and sub-operons, which are indicated by tsss within primary operons., promoter motifs were detected with the web-based tool improbizer [], which uses the expectation maximization (em) algorithm. for each tss, the 50 bases upstream were extracted and the −10 and −35 promoter motifs were searched within the sequences using […]

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

[…] ssigned to annotated genes were analyzed. all the genes with identified tss were considered in the analysis of tls and rbs motifs, for this analysis 50 base pairs upstream of tls were considered. the improbizer [] program was used to find the motifs and the tool weblogo [] was used to generate the visualization charts. in both programs, the default settings were applied for the analysis. in the te […]

PMCID: 5685739
PMID: 29163818
DOI: 10.18632/oncotarget.21621

[…] average linkage., the search for significantly over-represented motifs was done on mirnas identified as overexpressed in exosomes compared to cells for gscs and/or nscs using the online application improbizer (https://users.soe.ucsc.edu/~kent/improbizer/improbizer.html). as background we used the mirnas included on the arrays that were not identified as overexpressed., clustering of mirna […]

PMCID: 4745078
PMID: 26853706
DOI: 10.1038/srep20648

[…] place (http://www. dna.affrc.go.jp/ place/ signalup.html), tess (http://www.cbil.upenn.edu/cgi-bin/tess/tess) and pwm (http://users.soe.ucsc.edu/~kent/improbizer/motifmatcher.html)., how to cite this article: niu, j. et al. cross-talk between freezing response and signaling for regulatory transcriptions of mir475b and its targets by mir475b […]


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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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