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Protocols

CoGe specifications

Information


Unique identifier OMICS_30269
Name CoGe
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Documentation


Maintainer


  • person_outline SynFind

Additional information


https://genomevolution.org/wiki/index.php/Main_Page

CoGe citations

 (120)
library_books

Resolution effects in reconstructing ancestral genomes

2018
BMC Genomics
PMCID: 5954274
PMID: 29764371
DOI: 10.1186/s12864-018-4462-y

[…] roxy for the ancestral hexaploid [].The main data for this paper consists of three-way synteny blocks between grape, Rhazya and coffee. As a first step, we used SYNMAP, https://www.genomevolution.org/CoGe/SynMap.pl (with default parameters) in the CoGe platform https://genomevolution.org/CoGe/ to find pairwise synteny blocks between grape and Rhazya (806 blocks), between Rhazya and coffee (583 blo […]

library_books

Enhanced JBrowse plugins for epigenomics data visualization

2018
BMC Bioinformatics
PMCID: 5921565
PMID: 29699480
DOI: 10.1186/s12859-018-2160-z

[…] visualize these data sets effectively, hindering the visualization and potential discoveries with new sequencing technologies. JBrowse is used by numerous scientific resources, such as Phytozome [], CoGe [], WormBase [], and Araport [] because it is highly customizable and adaptable with modular plugins [].Epigenomics is an emerging area of research that generates a significant amount of speciali […]

library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] genome databases are well-maintained and are frequently updated with release of new versions, such as PlantGDB V187, Phytozome V12, and Gramene V36. Phytozome updates roughly each year, and PGDD and CoGe update timely upon availability of new genome data. Another feature is that these databases are empowered with various tools other than the open-sourced BLAST and browsers. They offer tools for g […]

library_books

A tutorial of diverse genome analysis tools found in the CoGe web platform using Plasmodium spp. as a model

2018
PMCID: 5887277
DOI: 10.1093/database/bay030

[…] Find SynMap on CoGe’s main page (https://genomevolution.org/CoGe/SynMap.pl).Search for and select the desired genome for Organisms 1 and 2 [e.g. type Plasmodium in the ‘Search’ box for Organism 1 and select P. falci […]

library_books

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

2018
PLoS Genet
PMCID: 5891031
PMID: 29590103
DOI: 10.1371/journal.pgen.1007267

[…] p plant Cleome violacea, which split from the six taxa studied prior to that event []: it likewise lacks the WGD found in other taxa in the Cleomaceae []. The C. violacea genome is available from the CoGe comparative genomics portal (https://genomevolution.org/coge/) under accession number 23822. For the grass ρ event, we used the genome of the pineapple Ananas comosus as an outgroup []. CoGe acce […]

library_books

Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage Based Selection on Homeologs Is Long Lived

2018
Genome Biol Evol
PMCID: 5887293
PMID: 29617811
DOI: 10.1093/gbe/evy061

[…] We obtained pairs of At-α duplicates using CoGe’s SynMap algorithm () and merged this list with the At-α duplicates reported by using version 10.02 of the Arabidopsis thaliana Col-0 genome as our reference (). We excluded from our ohnolog lis […]

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