Question: Is there a tool for making a synteny blocks of a gene with its downstream and upstream genes using a bacterial genome sequence?
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gravatar for sharmatina189059
12 weeks ago by
United States
sharmatina18905930 wrote:

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 • 229 views
ADD COMMENTlink modified 12 weeks ago by Joseph Hughes2.7k • written 12 weeks ago by sharmatina18905930

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by jean.elbers530

interesting link, thx.

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

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by lieven.sterck3.9k
1

Thanks- it is fixed now.

ADD REPLYlink written 12 weeks ago by jean.elbers530

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

ADD REPLYlink written 12 weeks ago by jrj.healey10k

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

ADD REPLYlink written 12 weeks ago by sharmatina18905930

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

ADD REPLYlink written 12 weeks ago by jrj.healey10k
0
gravatar for Joseph Hughes
12 weeks ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

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

ADD COMMENTlink written 12 weeks ago by Joseph Hughes2.7k
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