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The coffee genome hub: a resource for coffee genomes.

Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G - Nucleic Acids Res. (2014)

Bottom Line: The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released.It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor.In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.

View Article: PubMed Central - PubMed

Affiliation: UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.

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Management of SNP polymorphisms in the Coffee Genome Hub. (A) Users can retrieve polymorphic positions based on a subset of genotypes and a subset of genes. The database outputs SNPs together with annotations, minor allele frequency and genotypic data. (B) Connection with JBrowse allows visualizing and browsing the genomic location of the selected SNP. (C) Resulting SNPs can be sent to our tool that calculates and displays the distribution of SNP density on the genome or to a SNP-based distance tree analysis.
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Figure 3: Management of SNP polymorphisms in the Coffee Genome Hub. (A) Users can retrieve polymorphic positions based on a subset of genotypes and a subset of genes. The database outputs SNPs together with annotations, minor allele frequency and genotypic data. (B) Connection with JBrowse allows visualizing and browsing the genomic location of the selected SNP. (C) Resulting SNPs can be sent to our tool that calculates and displays the distribution of SNP density on the genome or to a SNP-based distance tree analysis.

Mentions: Examples of visualization in JBrowse are shown in Figures 1, 2 and 3.


The coffee genome hub: a resource for coffee genomes.

Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G - Nucleic Acids Res. (2014)

Management of SNP polymorphisms in the Coffee Genome Hub. (A) Users can retrieve polymorphic positions based on a subset of genotypes and a subset of genes. The database outputs SNPs together with annotations, minor allele frequency and genotypic data. (B) Connection with JBrowse allows visualizing and browsing the genomic location of the selected SNP. (C) Resulting SNPs can be sent to our tool that calculates and displays the distribution of SNP density on the genome or to a SNP-based distance tree analysis.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383925&req=5

Figure 3: Management of SNP polymorphisms in the Coffee Genome Hub. (A) Users can retrieve polymorphic positions based on a subset of genotypes and a subset of genes. The database outputs SNPs together with annotations, minor allele frequency and genotypic data. (B) Connection with JBrowse allows visualizing and browsing the genomic location of the selected SNP. (C) Resulting SNPs can be sent to our tool that calculates and displays the distribution of SNP density on the genome or to a SNP-based distance tree analysis.
Mentions: Examples of visualization in JBrowse are shown in Figures 1, 2 and 3.

Bottom Line: The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released.It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor.In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.

View Article: PubMed Central - PubMed

Affiliation: UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.

Show MeSH
Related in: MedlinePlus