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promoter analysis in plant

Hi

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 ?

gad plantcare script python result
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written by Nelo • Nelo

Can you link the GTF file? Essentially it is just getting the transcripts for that gene and then take 2kb upstream of each.

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written by ATpoint ATpoint

Hi

What(data) to link with GFF/GTF? Sorry I did not get it. Can you please explain a bit more

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written by Nelo • Nelo

Hi

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.

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written by Nelo • Nelo

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