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PubData specifications

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Unique identifier OMICS_12593
Name PubData
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline Bohdan B. Khomtchouk <>

Publication for PubData

PubData in publications

 (18)
PMCID: 5740181
PMID: 29269837
DOI: 10.1038/s41598-017-18277-y

[…] the two parents, were subjected to standard slaf-sequencing, which was performed as described previously with minor modifications. first, the reference genome of silkworm (http://sgp.dna.affrc.go.jp/pubdata/genomicsequences.html) was predicted using the software developed by biomarker (beijing) to select the suitable endonuclease pairs, rsai + hpy166ii. then, dna samples from the parents […]

PMCID: 5004587
PMID: 27576083
DOI: 10.1038/sdata.2016.73

[…] in data citation 5., for our analyses, a bombyx mori reference genome was assembled (data citation 4) by incorporating assembled scaffolds anchored to chromosomes (http://sgp.dna.affrc.go.jp/pubdata/genomicsequences.html) and genome contigs assembled to scaffolds, but not anchored to chromosomes. scaffolds that were less than 20 kb in length were excluded. the remaining sequences […]

PMCID: 4742824
PMID: 26847502
DOI: 10.1038/srep20229

[…] short read alignment software, the part of the b. mori genome that is assembled in scaffolds and anchored to chromosomes was retrieved from the public data repository (http://sgp.dna.affrc.go.jp/pubdata/genomicsequences.html) of kaikobase (http://sgp.dna.affrc.go.jp/kaikobase). then, b. mori genome contigs assembled to scaffolds but not anchored to chromosomes were also retrieved […]

PMCID: 5615833
PMID: 28959545
DOI: 10.1016/j.toxrep.2016.01.009

[…] non-proprietary johnson & johnson (janssen) toxicogenomics codelink database, available in normalized ratio format in collaboration with strand life sciences, pvt., ltd., at the weblink: http://pubdata.strandls.com/ in the folder “jnj codelink data/” ., raw data related to this project are also publically available in the cebs at the niehs website., to access the cebs website:•go […]

PMCID: 4652390
PMID: 26582032
DOI: 10.1186/s12864-015-2111-2

[…] to mapped features and define overlaps between features., the fantom5 human and mouse cage-derived promoters mapped to the pig genome (version 10.2) are provided to the users as a track hub (http://pubdata.roslin.ed.ac.uk/genomics/farm-animal/susscr3/suppdata/hub.txt) as well as the mappings of pig cage ctss and rna-seq datasets generated for this study to visualize in a genome browser. bed […]


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PubData institution(s)
Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA; Ransom Everglades School, Miami, FL, USA; Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Electrical and Computer Engineering, University of Miami, Miami, FL, USA

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