How to determine the sets of genes are side by side in genomes?

Question

[K.Gee]

Hello.

I determined some sets of core genes from 5 genomes (I used in combination blast search of genomes orfs against itself and MCL), and my target is to find which of those sets of genes are side by side in all five genomes. I did a tblastn search of those sets against that 5 genomes, but I wasn't able to figure it out. Does anyone have any idea how I can get through this task?

Thank you in advance!!!

[K.Gee]

I tried both of your recommendations, but I realized that it was not what I was looking for. Maybe I didn't describe what I want to do accurately. They stay that I was interested in called gene gangs. I found this paper for the gene gangs, and this is what I'm going to apply. But thank you @genomax @Mensur Dlakic for the answers.

[GenoMax]

side by side as in some defined order? You are working with Viral genomes that are contiguous? You could try out mauve (link) to see large scale organization.

[K.Gee]

First of all, thank you for the prompt reply. Yes, I'm working on viral genomes, and I would like to find out if those core gene sets stay together in all genomes or not.

[GenoMax]

Try the program I linked above in that case.

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[K.Gee]

ok, I see. Thank you very much once again. I will try the program and I 'll let you know by clicking on the tick button.

Answer 1

[Mensur Dlakic]

STRING does what you need. Use one of your proteins for the initial search and select the "Neighborhood" section of the output.

I already wrote the above before realizing that you are talking about viruses. Not sure if STRING works with viral genomes, but it is worth a try.

There are manual solutions for this problem, though they may be somewhat inelegant. For example, you can download all viral genomes of interest and search with your core genes concatenated into a single, continuous sequence. Any time you get a match that is similar in size to your whole sequence - and without any large gaps - would indicate that the same core genes are present in other genomes.

You can do the same with concatenated proteomes.