how to find homologous regions using genomic coordinates

Question

[Lila M]

Hello,

I have 3 lists of rearrangements (with their breakpoints), they are bed files. I would like to know if there is any tool to check the homology in those regions (among my files), ideally with no more than 50bp on either side of the breakpoints

Thanks

Answer 1

[Emily]

You could try the Ensembl REST API.

[Lila M]

Thank you for the tip, but I'm a bit confuse about how to use it, is there any tutorial or samithing for R ?

[Emily]

Online course including R here.

[Lila M]

Thhank you, I did the course but couldn't find the proper tool to achieve this issue, do you already know which tool should I use or do you write this "just in case it could be useful"? thank you

[Emily]

I've given you the exact REST API endpoint that you need and I've given you a link to an online course that shows you how to use that REST API overall (but not that specific endpoint) and has loads of code that you can recycle. These two pieces of information together should be perfectly sufficient.

The only way I can see to help you more would be to write a script for you, which I'm not going to do for two reasons:

1. That's not my job.
2. I don't know what you actually want to retrieve homology to or what species your start data is from. But mainly, the first reason.

I am happy to help troubleshoot any specific problems you have with your script.

[Lila M]

I don't want that anyone write a script for me or do my job. But if I undertand properly the example you sent me considers only a specific coordinates given and not a bounch of them stored in different files to check the homology among them.

[Emily]

Ah, you want to match between your files, not to known homology. Then I'm afraid I can't help you.

[Lila M]

Exactly, I want to know if there is any homology in my regions or around the breakage sites. This is why I asked for clarifications before, because with the information you sent, I was not able to resolve my problem