Genes on chromosome

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3.9 years ago

fatma.mokhtar ▴ 20

Hello,

Is there a simple program where you can enter a set of genes (I have 10 genes). and then you get the location of the gene on the chromosome in one figure. So a figure with 22 chromosomes contains my gene of interest?

Many thanks, Fatma Mokhtar

gene • 899 views

ADD COMMENT • link updated 3.9 years ago by lieven.sterck 15k • written 3.9 years ago by fatma.mokhtar ▴ 20

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Check out the karyoploteR package - the kpPlotMarkers functions looks useful. You'll need to use biomaRt or org.Hs.Eg.db to get coordinates for each gene.

ADD REPLY • link 3.9 years ago by Ram 43k

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If you want to try karyoploteR, you can find a tutorial page with the code you need at https://bernatgel.github.io/karyoploter_tutorial//Examples/PlotGenes/PlotGenes.html

ADD REPLY • link 3.9 years ago by bernatgel ★ 3.4k

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if it's a plant species you're working with you might have a look at PLAZA, especially the WGMapping tool: eg: https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_5_dicots/genome_mapping/index

ADD REPLY • link 3.9 years ago by lieven.sterck 15k

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NCBI's genome data viewer may fit the bill (if your genome is on their list).

ADD REPLY • link 3.9 years ago by GenoMax 141k

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Drawing Chromosome Ideograms With Data

ADD REPLY • link 3.9 years ago by Pierre Lindenbaum 161k

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