Entering edit mode
11 weeks ago
Nelo • 0
I did promoter analysis of Hsp20 of one plant species, for which I extract 2kb upstream sequences from each 40 Hsp20 genes that I found in that particular plant species.
GAD python script was used to extract this sequences (https://github.com/bio-projects/GAD / PMID: 32524530) and submitted to PlantCARE.
My question is : Is it possible to get a total of more than 2000 promoters for 50 Hsp20 in one particular species ???
If not . My doubt is this very tool (GAD python script) is giving me false result). Also, did anyone use this to extract upstream sequences ?
Can you link the GTF file? Essentially it is just getting the transcripts for that gene and then take 2kb upstream of each.
What(data) to link with GFF/GTF? Sorry I did not get it. Can you please explain a bit more
Sorry, my question was mistyped. The real question was "Is it possible to get approx. 2500 Cis-acting elements(CREs) during promoter analysis of ~50Hsp20 in a plant species" ?
*PlantCARE was used for identification of CREs by feeding those 2kb upstream sequences which I got from GAD tool.