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How to do synteny analysis between two bacterial genome?

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?

synteny genome de-novo
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updated by Joe Joe • written by Paul Paul

2 answers

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 Synima example output

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updated by Kevin Blighe Kevin Blighe • written by jean.elbers jean.elbers

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

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written by Paul Paul

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

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written by jean.elbers jean.elbers

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.

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?

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written by Joe Joe

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