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Protocols

zPicture specifications

Information


Unique identifier OMICS_21234
Name zPicture
Interface Web user interface
Restrictions to use None
Input data A sequence or gene annotation.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Lisa Stubbs

Additional information


https://zpicture.dcode.org/zpInstructions.html

Publication for zPicture

zPicture citations

 (33)
call_split

BMP3 expression by osteoblast lineage cells is regulated by canonical Wnt signaling

2017
FEBS Open Bio
PMCID: 5794463
PMID: 29435407
DOI: 10.1002/2211-5463.12347
call_split See protocol

[…] tp://www.hiv.lanl.gov/content/sequence/CONSENSUS/consensus.html) using ‘Output aligned’ parameter. For the identification of transcription factor binding sites, DNA sequences were first aligned using zpicture . […]

library_books

Origin and evolution of MIR1444 genes in Salicaceae

2017
Sci Rep
PMCID: 5223194
PMID: 28071760
DOI: 10.1038/srep39740

[…] rried out using DNAMAN. Phylogenetic tree was constructed using MEGA5.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Alignment of large genomic DNA segments was performed using zPicture (http://zpicture.dcode.org/) and Generic Synteny Browser (GBrowse-syn). […]

call_split

Genes Frequently Coexpressed with Hoxc8 Provide Insight into the Discovery of Target Genes

2016
Mol Cells
PMCID: 4870187
PMID: 27025388
DOI: 10.14348/molcells.2016.2311
call_split See protocol

[…] ne Ontology (GO) annotations with an enrichment score > 1.0, p-value < 0.01, and false discovery rate (FDR) ≤ 5% were considered biologically significant. We used the rVista sequence analyzer (http://zpicture.dcode.org/) to search for Hox consensus binding elements present in the 5 kb promoter, first exon, and first intron of putative target genes. The gene network was analyzed with Ingenuity Path […]

library_books

Long Noncoding RNA MHRT Protects Cardiomyocytes against H2O2 Induced Apoptosis

2016
PMCID: 4703348
PMID: 26759697
DOI: 10.4062/biomolther.2015.066

[…] HRT in the heart as a standard, the expressions of MHRT in the other organs were significantly lower (). Furthermore, we compared the MHRT sequence in human and mouse with software rVista 2.0 (http://zpicture.dcode.org/), the result showed that there is conserved sequence between human and mouse (), indicating that MHRT might exert its biological function in cardiomyocytes. […]

call_split

The AIRE 230Y Polymorphism Affects AIRE Transcriptional Activity: Potential Influence on AIRE Function in the Thymus

2015
PLoS One
PMCID: 4433237
PMID: 25978041
DOI: 10.1371/journal.pone.0127476
call_split See protocol

[…] on factor binding sites were identified using rVista 2.0 (all vertebrate matrices under “optimised for function” parameters) to analyse the human and chimpanzee sequences which had been aligned using zpicture [] www.dcode.org. […]

call_split

The Vertebrate RCAN Gene Family: Novel Insights into Evolution, Structure and Regulation

2014
PLoS One
PMCID: 3896409
PMID: 24465593
DOI: 10.1371/journal.pone.0085539
call_split See protocol

[…] hese alignments were subsequently edited using GeneDoc software (http://www.nrbsc.org/gfx/genedoc/) . Alignments and pip-type graphs of RCAN-associated antisense transcripts were achieved using multi-zPicture (http://zpicture.dcode.org/multiz.php) applying an ECR criteria of ≥10 pb; ≥50% ID. Transposable element sequences were identified using the CENSOR tool (http://www.girinst.org/censor/index. […]

Citations

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zPicture institution(s)
Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA, USA; Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA; Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA; Department of Biology, The Pennsylvania State University, University Park, PA, USA
zPicture funding source(s)
Supported by the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory Contract No. W-7405-Eng-48 and by NHGRI grant HG02238.

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