Genome wide study Part 8 | Genomic CDS Promoter sequences and GFF file

In this video, we use phytozome online database to download the genomic, CDS and promoter sequences of protein family from the plant specie genome to do different genome wide analysis like gene structure, promoter region analysis. We also download the GFF genomic and protein files of two different plant species to do the synteny analysis by using TBTool and also used to construct the gene structure
plant genome database

[NazeerAhmed-cm]

Really excellent and informative video. I learned how to use TBtool watching your videos.

[Noor-cerl]

Great work. I really appreciate your work and your behaviour to share your knowledge with others. I really enjoy the learning with you.

[matataboy]

AoA. First of all I would like to appreciate the great work you have done. Your videos are very informative, to the point and easy to understand. Keep up the great work.
I have a question though, I am working on fish species. can you please point out a website to retrieve all the required files like GFF for animal species. Thanks

[vijayrajamanickam]

May I know why you are selecting 12 sequence up from the end. But in interPro start and end is 9 to 618. I think selecting sequence from 9th is fine. But, selecting sequence 12 sequences up from the end instead of 618 is wrong or right?

[nikitatiwari]

hello sir.
can you please explain how we can retrieve promoter sequences of the multiple gene list

[priscillak]

This video is excellent but this is phytozome 12, Can you do it for phytozome 13

[Piyalimukh]

Where do you know that promoter is 1500 bp upstream?

[sridharshinisathishkumar]

Hello sir, on what basis u take 1500bps for viewing promotor region?? Plz reply as soon as possible thank you

[sheharbano]

I am not having access to Phytozome. No login access is available. Is there any way out if Phytozome doesn't work out. Please guide me regarding it. JazakAllah 💎

[vijayrajamanickam]

Could you please tell me on what basis you are selecting GFF file in the phytozome @11.39? Because all are looking same.

[hafizmuhammadahmad]

Sir i followed the procedure but im unable to open the gff file.

[ajlectures]

Dr sahb plz update information according to changed version of Phytozome

[stanyang]

Hello
This is urgent
What if plant species of my interest is not available in Phytozome, then from where can I get all the information like GFF, protein and genomic sequence from ?

[hafizmuhammadahmad]

Sir, kindly guide how to download these sequences in phytozome v13