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

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?

genome
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updated by Joseph Hughes Joseph Hughes • written by sharmatina189059 • sharmatina189059

interesting link, thx.

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

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written by lieven.sterck lieven.sterck

Thanks- it is fixed now.

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written by jean.elbers jean.elbers

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

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written by Joe Joe

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

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written by sharmatina189059 • sharmatina189059

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

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written by Joe Joe

1 answer

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

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written by Joseph Hughes Joseph Hughes

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