Is there a tool for making a synteny blocks of a gene with its downstream and upstream genes using a bacterial genome sequence?
1
0
Entering edit mode
6.0 years ago

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 • 2.2k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

interesting link, thx.

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

ADD REPLY
1
Entering edit mode

Thanks- it is fixed now.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
6.0 years ago
Joseph Hughes ★ 3.0k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1877 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6