MochiView protocols

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MochiView specifications

Information


Unique identifier OMICS_02174
Name MochiView
Alternative name Motif and Chip Viewer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.46
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MochiView

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Maintainer


  • person_outline Oliver Homann <>

Publication for Motif and Chip Viewer

MochiView in pipelines

 (5)
2017
PMCID: 5391208
PMID: 28327289
DOI: 10.7554/eLife.23250.025

[…] were generated using macs2 () with peak shift sizes generated using spp (). peaks were assigned to genes if any portion of the peak overlapped with the intergenic region upstream of that gene using mochiview (). for the heterologous p. pastoris ndt80 in s. cerevisiae chip, fold enrichment values were mapped to genes by taking the maximum fold enrichment value for each intergenic region […]

2016
PMCID: 4777133
PMID: 26772749
DOI: 10.1534/g3.115.024885

[…] values from the individual peaks was used. gene assignments, evaluation of overlap with previously published data sets, and determination of median macs2 fold enrichment values were performed using mochiview v1.46 ()., file s1 contains a list of the genomic locations and median fold enrichment of the wor4-gfp peaks in both white and opaque cells. file s2 contains mochiview image plots of 12 kb […]

2015
PMCID: 4325683
PMID: 25698879
DOI: 10.4137/BBI.S20751

[…] feature types are mrnas and non-protein coding rnas, like trnas, rrnas, snornas, snrnas, mirnas and other ncrnas. as output, mochi files are created for visualizing the results in the genome browser mochiview. the pipeline can be used via web page front end (https://www.uni-frankfurt.de/fb/fb15/institute/inst-3-mol-biowiss/ak-schleiff/cracpipe/). for details see ., the mace results are available […]

2015
PMCID: 4531262
PMID: 26153861
DOI: 10.1038/nature14613

[…] reads were indexed and aligned to the genome using bowtie 2. file types were manipulated using samtools, and peaks were called using macs. coverage and peak calls were visualized in mochiview. the chip experiment was performed with a total of three replicates on two separate days, and a single replicate was performed of the untagged control., k. lactis reporter strains […]

2015
PMCID: 4676285
PMID: 26670385
DOI: 10.1128/mBio.01947-15

[…] were present in both fur+ and iron-deficient cultures (dbchip []; p < 0.05) or did not visually conform to a peak above the local background. normalized chip-seq data files were visualized with mochiview (). the final peak list is given in  in the supplemental material. fur binding site motifs were constructed by analyzing the 100 bp upstream and downstream of the dpeak-identified peak […]


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MochiView in publications

 (25)
PMCID: 5414202
PMID: 28443644
DOI: 10.1038/ncomms15161

[…] motif enrichment analysis was performed using homer software. for all chip-seq data sets, wig files were generated with model-based analysis of chip-seq, which were subsequently visualized using mochiview v1.46. taz and h3k27ac chip-seq heatmaps were ordered by strength of binding. the heatmaps were drawn using the heatmap tools provided by cistrome (http://cistrome.org/ap)., all analyses […]

PMCID: 5345727
PMID: 28122954
DOI: 10.1534/g3.116.036939

[…] coli k-12 mg1655) using a custom-written perl script (file s1)., text files of processed ribo seq and mrna seq data, porf list, and salmonella genome annotation were uploaded to the genome browser mochiview () for visualization and manual inspection. for calculation of reads per kilo per million (rpkm) values for (un)annotated genes, clc genomics workbench (ver 8.0; qiagen) was used. […]

PMCID: 5446240
PMID: 28485712
DOI: 10.7554/eLife.25157.028

[…] cgpho4 binding sites into ones co-bound by cgpho2 or those bound by cgpho4 only., after the automatic peak calling, we manually curated the peaks with visual help from a genome browser tool, mochiview (rrid:scr_000259) (). we calculated a fold enrichment trace for each chip sample by comparing it to its matching input (or mock, in case of chip-exo), using macs2 following […]

PMCID: 5391208
PMID: 28327289
DOI: 10.7554/eLife.23250.025

[…] were generated using macs2 () with peak shift sizes generated using spp (). peaks were assigned to genes if any portion of the peak overlapped with the intergenic region upstream of that gene using mochiview (). for the heterologous p. pastoris ndt80 in s. cerevisiae chip, fold enrichment values were mapped to genes by taking the maximum fold enrichment value for each intergenic region […]

PMCID: 4889938
PMID: 27001516
DOI: 10.1093/nar/gkw180

[…] bowtie v.0.12.0. the alignment .map files were used as inputs for the modified python scripts(). the normalized ribosome densities, measured as reads per million reads (rpm), were visualized in mochiview (). the gene expression levels (reads per kilobase per million mapped reads, rpkm) were calculated using python scripts (). translation efficiency (te) was calculated as the relative number […]


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MochiView institution(s)
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
MochiView funding source(s)
Supported by NIH grant 5R01GM37049-22.

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