Step 1 — Promoter Extraction

Pulls the upstream region of every gene out of a genome FASTA, using the coordinates and strand information from a matching GFF3 annotation.

Inputs

Genome FASTA — any standard .fa / .fasta / .fa.gz.
Annotation GFF3 — NCBI RefSeq, Ensembl, or any GFF3 that contains gene features with ID= attributes.
Promoter length (bp) — default 2000.

What it does

For every gene feature in the GFF3:

Read the gene’s chromosome, start, end, and strand.
On the + strand, take [start - upstream, start).
On the - strand, take (end, end + upstream] and reverse-complement.
Clip at neighbouring gene boundaries (intergenic only) if the “Avoid overlapping genes” box is checked.

Output

promoters.fa — one entry per gene; FASTA header is the gene ID, optionally prefixed with chromosome and coordinate range.

CLI equivalent

cis-gs extract --fasta genome.fa --gff annot.gff3 \
               --upstream 2000 --avoid-overlap --out promoters.fa