Question: Is there a tool for making a synteny blocks of a gene with its downstream and upstream genes using a bacterial genome sequence?
0
gravatar for sharmatina189059
7 months ago by
United States
sharmatina18905940 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 • 395 views
ADD COMMENTlink modified 7 months ago by Joseph Hughes2.7k • written 7 months ago by sharmatina18905940

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 7 months ago • written 7 months ago by jean.elbers1.1k

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 7 months ago • written 7 months ago by lieven.sterck5.5k
1

Thanks- it is fixed now.

ADD REPLYlink written 7 months ago by jean.elbers1.1k

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

ADD REPLYlink written 7 months ago by jrj.healey13k

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

ADD REPLYlink written 7 months ago by sharmatina18905940

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

ADD REPLYlink written 7 months ago by jrj.healey13k
0
gravatar for Joseph Hughes
7 months 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 7 months ago by Joseph Hughes2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1456 users visited in the last hour