How to do synteny analysis between two bacterial genome?

Question

[Paul]

I have a novel bacterial genome of 8Mb length (Genome1), which I want to compare it with existing well annotated gram-negative bacterial genome (Genome2). Could anyone suggest me a way to check how many genes in my novel species are matching with well-annotated bacterial genome?

One option is to blast Genome 1 with Genome 2. However, How do I visualize? I tried using

Synteny portal http://bioinfo.konkuk.ac.kr/synteny_portal/htdocs/synteny_circos.php

but it shows graphs, with the existing genome in the database, we cannot upload any new sequences to do the comparison. :( Any Suggestions? Any web-based tool is available?

Answer 1

[jean.elbers]

I would recommend Synima ( https://github.com/rhysf/Synima ), but it requires that you have annotations for both: Genome 1 and Genome 2 in your case

edit: Below is an example output from Synima, just so you get an idea of what it can do

[Paul]

Thankyou.. will try it, any web-based tool available?

[jean.elbers]

Sorry, I don't know about any web-based tools, but the developer is very helpful with answering questions.

Answer 2

[Joe]

These aren't exact fits for what you're doing, but I really like sibelia and MultiGeneBlast for synteny/conservation work. Sibelia will write circos plots for you.

• http://bioinf.spbau.ru/sibelia
• http://multigeneblast.sourceforge.net/

MGB is more for finding operons in genomes, so I'm not sure how well it'll do with whole genome comparisons, but worth a go?