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Citations per year

Number of citations per year for the bioinformatics software tool GSV
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Tool usage distribution map

This map represents all the scientific publications referring to GSV per scientific context
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Popular tool citations

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Protocols

GSV specifications

Information


Unique identifier OMICS_00939
Name GSV
Alternative name Genome Synteny Viewer
Interface Web user interface
Restrictions to use None
Input data A mandatory genome synteny data file is required to use mGSV along with an optional genome annotation data file.
Output format Tab-delimited text
Programming languages Javascript, PHP
Database management system MySQL
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for Genome Synteny Viewer

GSV citations

 (17)
call_split

Sequencing and Analysis of Strobilanthes cusia (Nees) Kuntze Chloroplast Genome Revealed the Rare Simultaneous Contraction and Expansion of the Inverted Repeat Region in Angiosperm

2018
Front Plant Sci
PMCID: 5861152
PMID: 29593773
DOI: 10.3389/fpls.2018.00324
call_split See protocol

[…] samum indicum (NC_016433.2), and Scrophularia takesimensis (NC_026202.1) by using BLASTN with an E-value cutoff of 1e-10. The homologous regions and gene annotations were visualized using a web-based genome synteny viewer GSV (). […]

library_books

A high density consensus linkage map of white lupin highlights synteny with narrow leafed lupin and provides markers tagging key agronomic traits

2017
Sci Rep
PMCID: 5681670
PMID: 29127429
DOI: 10.1038/s41598-017-15625-w

[…] Linkage groups were drawn in MapChart. Sequence collinearity blocks were visualized using Genome Synteny Viewer, Circos and Legume Information System. […]

call_split

Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis

2017
PLoS One
PMCID: 5581003
PMID: 28863197
DOI: 10.1371/journal.pone.0184196
call_split See protocol

[…] using blastn program provided by EMBOSS. The detailed parameters were “blastn -query genome1.fasta -db genome2.fasta -out result.o -outfmt 7”. The homologous regions were visualized using a web-based genome synteny viewer GSV []. […]

library_books

Genome Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211

2017
Front Microbiol
PMCID: 5359284
PMID: 28377746
DOI: 10.3389/fmicb.2017.00411

[…] ary Figure ). Furthermore, a genome synteny analysis among these strains was performed with different criteria of identifying probable recombination blocks (such as e-value, base pair length etc.) in GSV (). Probable recombination regions were marked, and individual gene sequences from these regions were extracted and aligned with ClustalW in MEGA6 () for recombination study with RDP (). Three dif […]

call_split

The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis

2017
PLoS One
PMCID: 5291543
PMID: 28158318
DOI: 10.1371/journal.pone.0171264
call_split See protocol

[…] ished chloroplast genomes of other plants, including tobacco (Nicotiana tabacum NC_007500.1), Arabidopsis thaliana (NC_000932), poplar (Populus NC_009143) and mulberry (Moraceae NC_025772) species by GSV [] (http://cas-bioinfo.cas.unt.edu/gsv/homepage.php). Firstly, the sequences of all chloroplast sequences were pair-wise compared by BLAST (http://www.jurgott.org/linkage/LinkagePC.html). Then, sc […]

library_books

Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2

2016
BMC Genomics
PMCID: 5073747
PMID: 27769166
DOI: 10.1186/s12864-016-3150-z

[…] es producing alignments to numerous loci dispersed over many chromosomes were marked as repetitive and excluded from further analysis. Sequence collinearity blocks were visualized using the Web-based Genome Synteny Viewer [] and Circos [].All marker sequences from linkage groups NLL-10 and NLL-17 [, , ] were repeat-masked by RepeatMasker and Censor []. Masked sequences were then aligned to the L. […]


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GSV institution(s)
Department of Biological Sciences, University of North Texas, Denton, TX, USA; Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
GSV funding source(s)
This work was supported in part by NIH grant 1RC2HG005806-01 and by the Junior Faculty Summer Research Fellowship at University of North Texas.

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