Is there a tool for making a synteny blocks of a gene with its downstream and upstream genes using a bacterial genome sequence?

Question

[sharmatina189059]

Dear all I have some protein sequences and bacterial genomes. I need to have a figure showing a block diagram of upstream and dowstream genes of that particular gene within multiple bacterial genome. Is there any tool for making a synteny of one gene in multiple genomes of bacteria?

[jean.elbers]

This might be possible with Synima (https://github.com/rhysf/Synima ). You would just restrict the input files to the region you are interested in.

[lieven.sterck]

interesting link, thx.

there is a small typo in your link though (you added a ')' in the link address ;) ) Fixed by OP

[jean.elbers]

Thanks- it is fixed now.

[Joe]

Doesn't exactly fit the bill, but you may be interested in looking at MultiGeneBlast and/or Sibelia.

[sharmatina189059]

Hi Sibelia is used for comparing only two genomes. I can not use it for multiple genomes.

[Joe]

It can create multiple pairwise comparisons in a Circos plot, but as I said, may not exactly fit the bill anyway.

Answer 1

[Joseph Hughes]

Perhaps, something like genoplotR would do the trick. I found it useful for looking at synteny of genes in large virus genomes.