GenomeJack protocols

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GenomeJack specifications

Information


Unique identifier OMICS_02143
Name GenomeJack
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline GenomeJack <>

GenomeJack in pipelines

 (5)
2015
PMCID: 4322709
PMID: 25713569
DOI: 10.3389/fmicb.2015.00078

[…] numbers ap014565 and ap014566, respectively], bwa-sw (li and durbin, ), and samtools (li et al., ) software were used with the default parameters. the mapping data obtained were visualized with genomejack viewer software (mitsubishi space software, tokyo, japan), and the mean coverage, which means average value of coverage of short reads on a specific genomic region, was calculated using r […]

2014
PMCID: 4262374
PMID: 25574134
DOI: 10.4137/GRSB.S19711

[…] tool of strand ngs that classifies the locations into the upstream region, 5′ untranslated region (5′utr), exon, intron, and 3′utr. we also imported the processed data into a genome viewer named genomejack v1.4 (mit-subishi space software). we identified the consensus motif sequences in the genomic regions surrounding the peaks by using the gadem program., to identify molecular networks […]

2013
PMCID: 3623615
PMID: 23645984
DOI: 10.4137/GRSB.S11433

[…] mapping them on hg19, we identified totally 3,744 stringent chip-seq peaks that meet the criteria of fold enrichment ≥20 and fdr ≤1%. the genomic locations of the peaks were determined by using genomejack (, panels a and b). we omitted the peaks located in non-coding genes (n = 157), those in intergenic regions (n = 1917), and redundant genes. finally, we identified 1,441 chip-seq peaks […]

2013
PMCID: 3623615
PMID: 23645984
DOI: 10.4137/GRSB.S11433

[…] fold enrichment ≥20 and the false discovery rate (fdr) ≤1%, according to the methods described previously. next, we identified genomic locations of macs peaks by importing the processed data into genomejack v1.3, a novel genome viewer for ngs platforms developed by mitsubishi space software (www.mss.co.jp/businessfield/bioinformatics). based on refseq id, macs peaks were categorized […]

2013
PMCID: 3825669
PMID: 24250222
DOI: 10.4137/GRSB.S13204

[…] are defined by refseqgene (http://www.ncbi.nlm.nih.gov/refseq/rsg). the consensus motif sequences surrounding a 400 bp-length sequence of the peak summits, extracted from the hg19 sequence track of genomejack, were identified by the meme-chip program., to identify the pathways biologically relevant to chip-seq-based nrf1 target genes, we imported the corresponding entrez gene ids […]


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GenomeJack in publications

 (7)
PMCID: 5884625
PMID: 29554130
DOI: 10.1371/journal.ppat.1006882

[…] calculated by bedtools (v. 2.17.0) [] and normalized by reads per kilobase of exon per million mapped reads (rpkm) according to the method by weedall et al []. the mapping data were visualized with genomejack viewer software (v 3.1) (mitsubishi space software, tokyo, japan) (http://genomejack.net/english/index.html). the predicted gene copy number was calculated at rpkm score of each gene […]

PMCID: 5304155
PMID: 28211918
DOI: 10.1038/srep42522

[…] on chromosome 19 (ch19):46273584-46273607 (ctcf_1) and ch19:46273339-46273360 (ctcf_2). finally, we performed a quantitative assessment using manorm. all the above results are shown in using the genomejack browser (mitsubishi space software corporation, tokyo, japan)., how to cite this article: ueki, j. et al. myotonic dystrophy type 1 patient-derived ipscs for the investigation of ctg […]

PMCID: 4492933
PMID: 26148004
DOI: 10.1371/journal.pone.0132030

[…] the reads and taking the consensus sequence. mapping was performed using the bwa (version 0.6.1) [] and samtools (version 0.1.18) [] software and visualized using the igv (version 2.0.34) [] and genomejack (version 2.1, mitsubishi space software) software. the mapping to a circular contig was performed by cutting a linear contig at different sites., mitochondrial genome contigs […]

PMCID: 4437538
PMID: 26023283
DOI: 10.4137/JCNSD.S23210

[…] sequences surrounding the peaks by using the gadem program and the genomic location of binding peaks by a peak-finding tool of strand ngs. we imported the processed data into a genome viewer named genomejack v1.4 (mitsubishi space software). for rna-seq analysis, after removing poly-a tails and low-quality reads from ngs short-read data, we mapped them on mm9 or hg19 by tophat version 2.0.9 […]

PMCID: 4262374
PMID: 25574134
DOI: 10.4137/GRSB.S19711

[…] tool of strand ngs that classifies the locations into the upstream region, 5′ untranslated region (5′utr), exon, intron, and 3′utr. we also imported the processed data into a genome viewer named genomejack v1.4 (mit-subishi space software). we identified the consensus motif sequences in the genomic regions surrounding the peaks by using the gadem program., to identify molecular networks […]


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GenomeJack institution(s)
Mitsubishi Space Software Company Limited, Tokyo, Japan

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