Question: How to write code to extract e.g. 1kb upstream of desired sequence to obtain promoter sequences for analysis?
0
gravatar for Monika515
2.3 years ago by
Monika5150
Monika5150 wrote:

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 • 1.0k views
ADD COMMENTlink modified 2.3 years ago by Nicolas Rosewick8.8k • written 2.3 years ago by Monika5150

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by RamRS27k
1
gravatar for Nicolas Rosewick
2.3 years ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

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)

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Nicolas Rosewick8.8k

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

ADD REPLYlink written 2.2 years ago by lilly10
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