How to write code to extract e.g. 1kb upstream of desired sequence to obtain promoter sequences for analysis?

Question

[Monika515]

I will be working with a specific human gene (let's call it X), for which I am to predict possible transcription factors. For this I want to work with the promoter sequences instead of the actual gene sequences. I am familiar with how to extract sequences in Biopython. I am rather new to coding and was wondering how would I be able to easily extract the promoters for each of the genes I obtain with a e.g. BLAST search to later e.g. do phylogenetic footprinting?

I am at a loss as to where to begin. I will happily take any advice and any guidance to useful resources from which I can learn. The Biopython tutorial/cookbook is rather useful but I have not been able to easily locate an answer to my question.

[Ram]

This post was deleted for some reason. @Monika515 - if Nicolas Rosewick's answer is useful, please accept their answer to mark the post as solved.

See: How to: Marki an answer as an accepted answer

Answer 1

[Nicolas Rosewick]

If you have the gene id you can easily extract the upstream sequence using ENSEMBL Biomart : https://www.ensembl.org/biomart/martview

Choose ENSEMBL GENES / Human genes (if you work in human)

Then Filters > Gene > "Input external references ID list" . Here put your gene id of interest and choose the correct type of gene id (ENSEMBL id, gene symbol, etc...)

Then Attributes > Sequences > Flank (Gene)

Click on upstream flank and put the number of desired upstream bases to extract (e.g. 1000 for 1kb)

Click on Results button (top left, just under ENSEMBL logo)

[lilly]

how to extract promoter regions around TSSs (−1500 to +500) using ENSEMBL Biomart?