How to extract all promoter regions in multi-fasta format from genome using GFF?

Question

[rimgubaev]

Hi Everyone,

How can I extract promoter sequences (ca. 1000bp upstream TSS) in multi-fasta format from genome (also multi-fasta with scaffolds) using information from corresponding GFF file? I've already tried to use GFF-Ex tool, however it didn't help (finished with errors). It is tobacco genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/715/135/GCF_000715135.1_Ntab-TN90/).

Does anyone know some other tools for this?

Thanks,

Answer 1

[rimgubaev]

Finally, I've solved this problem by combining samtools, bedtools as well as custom R script. The pipline placed into bash script is available here.

Answer 2

[shoujun.gu]

1. extract the gene id from GFF file
2. fetch the promoter sequence from BioMart by using the gene id you extracted

[GenoMax]

BioMart on Ensembl only appears to have Nicotiana attenuata genome but not the one OP likely wants.

[rimgubaev]

genomax is right there are no Nicotiana tabacum data on Ensembl.