GBrowse_syn protocols

GBrowse_syn specifications

Information


Unique identifier OMICS_00935
Name GBrowse_syn
Alternative name Generic Synteny Browser
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for Generic Synteny Browser

GBrowse_syn IN pipelines

 (3)
2014
PMCID: 4169385
PMID: 25232843
DOI: 10.1371/journal.pgen.1004660

[…] regions of c. congregata [27], [41], [95]. groups of orthologous genes (syntenic) in the genome were identified using the orthomcl output with orthocluster [96]. syntenic regions were viewed with gbrowse syn. assembly of the m. demolitor genome initially suggested the nudivirus-like gene cluster contained two identical duplications absent from the nudivirus-like gene cluster identified […]

2014
PMCID: 4210507
PMID: 25306241
DOI: 10.1186/1471-2164-15-891

[…] other genomes were covered at 86.5%, 89.5% and 87.3% for ibcn84, ibcn65 and b3.5, respectively. genomic alignments were performed with mavid and loaded with genome annotations in mysql databases. gbrowse-syn was configured to display the blocks of synteny (http://urgi.versailles.inra.fr/gb2/gbrowse_syn/leptosphaeria_synteny/)., an aggregative hierarchical clustering procedure was performed […]

2014
PMCID: 4210507
PMID: 25306241
DOI: 10.1186/1471-2164-15-891

[…] genomic alignments were performed with mavid and loaded with genome annotations in mysql databases. gbrowse-syn was configured to display the blocks of synteny (http://urgi.versailles.inra.fr/gb2/gbrowse_syn/leptosphaeria_synteny/)., an aggregative hierarchical clustering procedure was performed on all versus all blastp results from protein sequences of 80 annotated genomes at ncbi […]

GBrowse_syn institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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