Hello, First of please forgive me I have little knowledge in the subject, I'm coming from a computer science only background.
I'm building a webservice around ensembl rest api, so far all is good until I needed to get an exon only sequence.
What I'm trying to do is giving coordinates for example: human:10:101654703-101659823:-1 is 1- getting the sequence from the ensembl rest api. [easy enough] 2- getting overlapping exons that are protein coding in that region. example from the api 3- using the start and end of exons to get the whole overlapping sequence.
Now here are the problem I'm facing: 1- I believe there are different sources for exons(ensembl, ensembl_havana, havana). Which should I use and how? atm I'm prioritizing ensembl_havana and using that only, but I believe that is incorrect since ensembl_havana means exons that are agreed upon by both teams so I should add the rest of the exons reported by one of the teams to that ?
2- What's an Exon rank? didn't find information about that.
3- Given a negative strand and positive strand exons what to do and vice versa?
4- What's the Exon version ?
I apologise again for the amount of questions, but I've been struggling for a week with this, I'm getting valid results and more invalid ones.