GSV pipeline

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


This tool is not available anymore.

Publication for Genome Synteny Viewer

GSV IN pipelines

 (4)
2016
PMCID: 4969343
PMID: 27168155
DOI: 10.1007/s10577-016-9526-8

[…] parameters: e-value cutoff, 1e-20; word size, 8; gap existence cost, 5; gap elongation cost, 2; and nucleotide match/mismatch scores, 1/−2. microsyntenic blocks were visualized using the web-based genome synteny viewer (revanna et al. 2011) and circos (krzywinski et al. 2009)., primers for molecular markers amplification were designed based on bess with the use of primer3 plus software […]

2015
PMCID: 4404975
PMID: 25954293
DOI: 10.3389/fpls.2015.00268

[…] parameters: e-value cut-off, 1e-20; word size, 8; gap existence cost, 5; gap elongation cost, 2; nucleotide match/mismatch scores, 1/-2. microsyntenic blocks were visualized using the web-based genome synteny viewer (revanna et al., 2011). the synmap analysis tool was used (https://genomevolution.org/coge/synmap.pl) to determine if identified syntenic loci were located in large conserved […]

2013
PMCID: 4015606
PMID: 24148351
DOI: 10.1186/1742-4682-10-61

[…] (mp) methods were used for tree reconstruction. bootstrap analysis was done to check the reliability of trees. synteny analysis was performed using ensemble synteny view in ensemble database and genome synteny viewer (gsv)., evolutionary time for single gene trees showed that cenpj (0.02) evolving rapidly while cdk5rap2 (0.1) evolving with least rate as compare to other genes. all trees […]

2013
PMCID: 4015606
PMID: 24148351
DOI: 10.1186/1742-4682-10-61

[…] for tree reconstruction. bootstrap analysis was done to check the reliability of trees. synteny analysis was performed using ensemble synteny view in ensemble database and genome synteny viewer (gsv)., evolutionary time for single gene trees showed that cenpj (0.02) evolving rapidly while cdk5rap2 (0.1) evolving with least rate as compare to other genes. all trees were reconciling […]

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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