Comparative analyses of non coding genetic sequences

Question

[José]

Hi everyone,

I am conducting comparative analyses on non-coding sequences and need some advice. Should I remove all exons from my sequences, including those from alternative splicing isoforms, or only the exons that translate the primary protein isoform?

What is the best practice in this scenario?

Thanks for your help!

[Ram]

Please do not use bioinformatics as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see Forum and News type posts under https://www.biostars.org/tag/bioinformatics/

I've removed the tag this time but please be more mindful in the future.

[atharvakarkare14]

What's the end goal of your project? If you are looking into novel sequences then remove all the exons.