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

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.

sequence gene
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updated by Nicolas Rosewick Nicolas Rosewick • written by Monika515 • Monika515

1 answer

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)

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written by Nicolas Rosewick Nicolas Rosewick

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

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written by lilly • lilly

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