The most basic input for Promoter Prediction is a DNA sequence with a minimal length of 75bp
This sequence should be stored in a FASTA file with the extension .fna or .fasta. Other formats will be ignored by the web server.
Example of a FASTA sequence:
the first line is the header and all the lines below is the DNA sequence
Example of a FASTA file
with 100,000 bases: S_aureus_USA300_TCH1516_100k.fna
The web server is limited to one FASTA file containing one header.
The web server is limited to 200,000bp
For multiple or large sequences use the stand-alone version.
If a proper FASTA is uploaded, the web server will show a summery of the content. For the example above this will be:
FASTA header: >CP000730.1
DNA length: 99920
Once the FASTA is uploaded the "START ANALYSIS" button will appear showing that your input is ready to be analyzed
An annotation file is optional but will highly improve the interpretation and visualization of the results.
The most common annotation format is the Generic Feature Format version 3: GFF3 or GFF
Example of a GFF file
The web server will accept both file extensions; .gff or .gff3