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MapView specifications

Information


Unique identifier OMICS_00888
Name MapView
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability No
Maintained No

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Publication for MapView

MapView in pipelines

 (9)
2018
PMCID: 5791963
PMID: 29385200
DOI: 10.1371/journal.pone.0191205

[…] []). all identified genes were compared to those reported previously [,]. newly identified genes were confirmed using blast search of dog genomic sequences (available at ncbi.nlm.nih.gov/projects/mapview, []) and/or dog blat search (available at genome.ucsc.edu, []), using the canfam3.1 assembly (genbank assembly id gca_000002285.2)., for cll cases, genomic dna was extracted from 200 μl […]

2018
PMCID: 5851690
PMID: 29368091
DOI: 10.1007/s00335-018-9735-x

[…] nucmer was run with the—mum option. the resulting delta files were filtered for 1-to-1 alignments allowing for rearrangements, and the filtered delta files translated to coordinates to be used in mapview for plotting. the filtered delta files were also run through dnadiff., the zebrafish genome (1.5 gb) is roughly half the size of the human (3.3 gb) or mouse (2.8 gb) genome. to date, […]

2015
PMCID: 4391551
PMID: 25855651
DOI: 10.1534/genetics.114.173849

[…] http://genome.ucsc.edu/cgi-bin/hggateway?hgsid=409674941_iubyp8af1uoasctcb3qi2e3t1kff&clade=vertebrate&org=medaka&db=0, and http://viewer.shigen.info/medakavw/mapview/). the medaka reference genome sequence is based on the hd-rrii1 inbred line. in addition, the genome sequence of the hni-ii, kaga, hsok and nilan and kiyosu strains () are available […]

2015
PMCID: 4467842
PMID: 26076481
DOI: 10.1371/journal.pone.0130188

[…] (retnl, e.g., retnlb) coding and genomic sequences were identified in genomic databases maintained by the national center for biotechnology information (ncbi, www.ncbi.nlm.nih.gov/projects/mapview/) and ensembl (www.ensembl.org and www.pre.ensembl.org) in december 2014, using approaches we have used in previous studies [,,]. initial sequences were identified through searches […]

call_split

IMA Genome F 4

2015
PMCID: 4500086
PMID: 26203426
DOI: 10.5598/imafungus.2015.06.01.15

[…] v. 1.21 (), with the source designated as mitochondrial and the genetic code as yeast mitochondrial (). the mitochondrial assembly was compared with r. solani rhs1ap using the promer, showcoords, mapview, and mummerplot functions in mummer v. 3.23 (). all blast searches in this work were performed with an e-value threshold of 1.0e-5., the nuclear genome assembly of limonomyces culmigenus cbs […]


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MapView in publications

 (226)
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] (ashgenome.org/) includes the blast, jbrowse tools, and data download service. the jujube (ziziphus jujuba) genome database (jujube.genomics.cn/page/species/index.jsp) has tools such as gene search, mapview and blast. the limited availability of bioinformatic tools may have reduced the popularity and usability of these databases., constrution a comprehensive database requires the knowledge […]

PMCID: 5883343
PMID: 29636822
DOI: 10.1186/s13039-018-0371-7

[…] within the 6.0-mb genomic region, 9 of which are indicated to be disease genes in the online mendelian inheritance in man (omim) database according to ncbi map viewer (https://www.ncbi.nlm.nih.gov/mapview). the details of these 9 omim disease genes and their clinical characteristics and inheritances are shown in table . we analysed the dominant genes for potential dose-effect phenotypes. […]

PMCID: 5807450
PMID: 29426907
DOI: 10.1038/s41598-018-21136-z

[…] point (pi), were obtained from expasy proteomics server (http://web.expasy.org/compute_pi/)., chromosomal localization data was retrieved from ncbi map viewer (https://www.arabidopsis.org/mapview/). genes were mapped to the chromosomes using mapdraw. these genes were renamed from fvbhlh1 to fvbhlh113 according to their position, from the top to bottom, on the f. vesca chromosome,. […]

PMCID: 5785999
PMID: 29374218
DOI: 10.1038/s41598-018-19954-2

[…] of those, 65 initially did not have an annotation in ensembl 83. screening of the national center for biotechnology information (ncbi) bos taurus annotation (https://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9913&build=104.0) for those 65 loci enabled assignment of a predicted gene identifier for 10 of the loci. thus, 55 loci for which there was no prior information […]

PMCID: 5784091
PMID: 29367635
DOI: 10.1038/s41598-018-20013-z

[…] (phase shift) surface mapping microscope on the highest magnification setting (x101.61 magnification) (omniscan, uk). analysis was carried out using ex mode. the image analysis software used was mapview ae 2æ17 (z range 210.5–1.169 μm) (omniscan, uk)., to monitor cell viability, cells retained on surfaces were treated using a live/dead stain (live/dead™ baclight™ bacteria viability kit, […]


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MapView institution(s)
State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China; School of Manufacturing Science and Engineering, Sichuan University, Chengdu, China
MapView funding source(s)
Supported by National Basic Research Program of China (2007CB815701); National Natural Science Foundation of China (30730008, 30800060, 30600064 and 40876075).

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