Question: Tools to generate Genetic Context in Bacterial Genomes
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gravatar for Optimist
9 months ago by
Optimist90
India
Optimist90 wrote:

Could someone help me with a tool to generate genetic context images between two or multiple genomes.

Thanks in advance

plot synteny genomic context • 236 views
ADD COMMENTlink modified 8 months ago by Joe18k • written 9 months ago by Optimist90

What do you mean by "genetic context"? Can you show us an example of the type of image you're looking for, please?

ADD REPLYlink modified 9 months ago • written 9 months ago by Emily_Ensembl21k

Dear Emily, Thank You for the prompt response.

I would like to make an image with the Genetic Context of particular region of a bacterial genome. I would like to know if there is a tool that can help me generate the image. Link to reference image

ADD REPLYlink written 9 months ago by Optimist90

I am sorry but that is no clarification at all! What is the Genetic Context? The sequence? the genes?

ADD REPLYlink written 8 months ago by Michael Dondrup47k

Dear Micheal Dondrup,

Please see the image for reference.

Thank You

ADD REPLYlink written 8 months ago by Optimist90
1
gravatar for Joe
8 months ago by
Joe18k
United Kingdom
Joe18k wrote:

EasyFig can generate such images.

MultiGeneBlast and Sibelia can also provide somewhat similar outputs.

Have a look here: Interesting/useful/beautiful bio sequence viz tools

ADD COMMENTlink written 8 months ago by Joe18k
1
gravatar for Michael Dondrup
8 months ago by
Bergen, Norway
Michael Dondrup47k wrote:

So, what you want is a synteny plot. Have you tried SimpleSynteny. There are many tools for this task, but maybe an easy web-based one will do. Be prepared to have to wait a while for the BLAST runs to continue. To shorten the runs, make sure to trim the genomic contigs to the region of interest, and include only the genes that should be depicted in the image.

Publication:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987899

ADD COMMENTlink written 8 months ago by Michael Dondrup47k
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