promoter analysis in plant

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22 months ago

Nelo ▴ 20

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 • 859 views

ADD COMMENT • link 21 months ago by Nelo ▴ 20

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

ADD REPLY • link 22 months ago by ATpoint 85k

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Hi

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

ADD REPLY • link 22 months ago by Nelo ▴ 20

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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.

ADD REPLY • link 21 months ago by Nelo ▴ 20

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