Tools to generate Genetic Context in Bacterial Genomes

Question

[Optimist]

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

Thanks in advance

[Emily]

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

[Optimist]

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

[Michael]

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

[Optimist]

Dear Micheal Dondrup,

Please see the image for reference.

Thank You

Answer 1

[Joe]

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

Answer 2

[Michael]

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