Genome wide study Part 13 | Promoter region analysis using Plantcare | Cis regulatory element

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  • เผยแพร่เมื่อ 5 ธ.ค. 2024

ความคิดเห็น • 84

  • @funnyworld_19
    @funnyworld_19 11 หลายเดือนก่อน +2

    Dr sab I really appreciate your efforts because this video is very clear to understand.

    • @genomewidestudy
      @genomewidestudy  11 หลายเดือนก่อน

      Thanks for like and comment.

  • @sohelsgalleryjust5290
    @sohelsgalleryjust5290 ปีที่แล้ว +2

    Some times TBtools visualization result shows cis elements are outside the line of gene. How can I solve this problem? Please help me sir.

    • @genomewidestudy
      @genomewidestudy  ปีที่แล้ว

      Thanks for comment. your promoter length is smaller than the cis element position. May be some digits were deleted during file preparation. Please check your input file.

  • @saraseyf-u2j
    @saraseyf-u2j 10 หลายเดือนก่อน +1

    Hello Dr, thank you for your helpful video. I have a problem with TBtools, I want to use TBtools for analyzing promoters, but its error is: TBtools cant find gene with name. what should i do?

    • @genomewidestudy
      @genomewidestudy  10 หลายเดือนก่อน

      Gene Names in length file and in element file must be same. Check the gene names

  • @stanzinstan6669
    @stanzinstan6669 2 ปีที่แล้ว +3

    Hlo sir
    Can you please make a video on SDPpred tools to determine the specificity determining position in protein
    Tnks in advance

    • @genomewidestudy
      @genomewidestudy  ปีที่แล้ว

      Already made the video SDPpred. you can find from the video list by title
      #SDPpred Prediction of Functional amino acids in Protein sequence | SDPred for specific protein site

  • @logghoriaya6470
    @logghoriaya6470 ปีที่แล้ว +1

    Greetings! I want to clear something that if somone is working on abiotic stress related thing etc., then what to erase in the excel sheet(description)

  • @meenakshidangwal9851
    @meenakshidangwal9851 ปีที่แล้ว +1

    @genome Wide Study How can we show the position of cis elements in positive or negative strands?

    • @genomewidestudy
      @genomewidestudy  ปีที่แล้ว

      You get the position of cis element in the data from PlantCARE. You can use that data to show the position

  • @AvnishRaghuvanshi
    @AvnishRaghuvanshi 2 ปีที่แล้ว +1

    Dear doc,
    Nice presentation. I have an issue. when I download CARE result file, it shows its own id not my submitted protein Ids. And that's why tbtool is not producing the graphical presentations. How can I correct it?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      Follow the video and input method step by step..

  • @vijayrajamanickam6847
    @vijayrajamanickam6847 ปีที่แล้ว +1

    I am not able to open the Motif analysis result file which is downloaded from the email. The result file always saved as RSTUDIO file. What to do in this case?

  • @danielepinheiro4165
    @danielepinheiro4165 3 หลายเดือนก่อน +1

    After I press start, it appears the message that tbtool can`t find the promoters. What could be the error?the names are the same in both files.

    • @genomewidestudy
      @genomewidestudy  3 หลายเดือนก่อน

      Follow each step, don't skip the video. then you will solve your problem

  • @MaryamRiaz-e8g
    @MaryamRiaz-e8g 9 วันที่ผ่านมา

    For insects also plant care use for cis trans regulatory element?

  • @stanzinstan6669
    @stanzinstan6669 2 ปีที่แล้ว +1

    Sir what about those CREs which have no description about it functions like unbamed 1 , 4 etc. Can we exclude those

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      You can exclude in the figure but must keep in the table..

    • @stanzinstan6669
      @stanzinstan6669 2 ปีที่แล้ว

      @@genomewidestudy okie sir
      I am getting a total of approx 3000 CREs for 50 genes including both TATA box and those without function description.........it's 🆗 ?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      Yes.. Its good

    • @stanzinstan6669
      @stanzinstan6669 2 ปีที่แล้ว

      @@genomewidestudy Tnkq sir for ua support

  • @JaveriaSeyal
    @JaveriaSeyal 11 หลายเดือนก่อน +1

    How to download this excel sheet file ?
    And this exel sheet can be used for all the gene families or it is just for HSP70 family?

    • @genomewidestudy
      @genomewidestudy  11 หลายเดือนก่อน

      yes, you can use it for other gene families as well.

    • @genomewidestudy
      @genomewidestudy  11 หลายเดือนก่อน

      Go to the supplementary data of the paper, then download the required file

  • @ackahmichael449
    @ackahmichael449 ปีที่แล้ว

    Well done for your wonder works. Please can you confirm for me if I can submit batch promoter sequences now into Plant care database. I tried to submit all my 74 genes promoter sequences with faster format with the gene IDs but the plant are database always reject the approach. Please, I need help. Thank you.

    • @genomewidestudy
      @genomewidestudy  ปีที่แล้ว

      carefully check your data file, there must be missing of > sign with some IDs

  • @ribalmasri9415
    @ribalmasri9415 3 ปีที่แล้ว +1

    Please help doctor: in basic biosequence view, i am not getting anything after pressing start !!! what is the problem ?? thank you

  • @OscarMitalo
    @OscarMitalo 2 ปีที่แล้ว +1

    Hello, I have failed to install TBtools software on my MacBook Pro. Do you know of any possible solution for this?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      Download the related version, then install

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      Video about how to download and install tbtool
      has been uploaded. I think you will get help from it.

  • @nuravc5233
    @nuravc5233 2 ปีที่แล้ว +1

    hello, I want to ask something, when the promoter region in the genome sequence in phytosome is reversed, should it be taken from 1500 upstream or downstream?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      Upstream.. Because that upstream means, genes upstream, not the strand.

    • @nuravc5233
      @nuravc5233 2 ปีที่แล้ว

      @@genomewidestudy thank you :))

  • @rinkumalviya6722
    @rinkumalviya6722 2 ปีที่แล้ว +1

    How to make cis elements graphics with multiple gene in tbtools....?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      It is already described within the video, Please watch complete video, you will find your answer. Thanks

  • @stanzinstan6669
    @stanzinstan6669 2 ปีที่แล้ว +1

    Good veng doc
    How about trans-regulatory elements.....are they also present in the promoter regions and what are their functions ?

    • @genomewidestudy
      @genomewidestudy  2 ปีที่แล้ว

      I think literature is full of such type of information. Any how I will upload the video soon on this topic. Thanks for comment

    • @stanzinstan6669
      @stanzinstan6669 2 ปีที่แล้ว

      @@genomewidestudy tnkq
      Plz upload the video soon

  • @bilalfayaz892
    @bilalfayaz892 10 หลายเดือนก่อน

    Hlo sir…after putting the sequence name and details in basic bio sequence view there is showing debug log and iam not getting the element figure…..what is the problem??? Thanks in advance

    • @genomewidestudy
      @genomewidestudy  10 หลายเดือนก่อน

      Gene name in both files must be same and don't use the space bar to separate two words or figures. Use Tab

  • @kennethomondi904
    @kennethomondi904 3 ปีที่แล้ว +1

    Great presentation

  • @mahakhan4468
    @mahakhan4468 4 ปีที่แล้ว +2

    Nice presentation

  • @stanzinstan6669
    @stanzinstan6669 2 ปีที่แล้ว +1

    Great tutorial.....
    Is there any script or command line tool to extract or download upstream/downstream regions ?

  • @JaveriaSeyal
    @JaveriaSeyal 11 หลายเดือนก่อน

    After setting both files on tb tool , and clicking on start ...Debung log appears . How to solve it?

    • @genomewidestudy
      @genomewidestudy  11 หลายเดือนก่อน

      Tbtool did not recognize the space between two figures or words, so use tab. there must be a space. So check your input file

    • @JaveriaSeyal
      @JaveriaSeyal 11 หลายเดือนก่อน

      ​@@genomewidestudyok

  • @ahtishamali5070
    @ahtishamali5070 ปีที่แล้ว

    Assalm o alikum. hope you are fine there is an error occur during analysis on the Plant Care database. the message come is that "the reference contains illegal characters, please revise (only alpha-numeric allowed)"
    kindly guide me regarding this.

    • @genomewidestudy
      @genomewidestudy  ปีที่แล้ว

      May be your sequence have other than ATCG bases, like N or other. Check the sequence

  • @bipinkb8606
    @bipinkb8606 2 ปีที่แล้ว +1

    when i press start it is showing "debug log" why this is happening?

  • @muhammadateeq7744
    @muhammadateeq7744 3 ปีที่แล้ว +1

    Informative

  • @zamarudshah9147
    @zamarudshah9147 4 ปีที่แล้ว +1

    Informative..

  • @silvanalorenamiras1570
    @silvanalorenamiras1570 ปีที่แล้ว +1

    This tool is not working, what ever I do

  • @mominamalik1304
    @mominamalik1304 2 ปีที่แล้ว

    thank you sir

  • @mohammadhasan4945
    @mohammadhasan4945 หลายเดือนก่อน +1

    Good

  • @mdmustafizurrahman7693
    @mdmustafizurrahman7693 3 ปีที่แล้ว

    Can I get the excel sheet?

    • @genomewidestudy
      @genomewidestudy  3 ปีที่แล้ว

      Yes you can download from the supplementary material of the manuscript, I have acknowledged in the video

  • @mohammadasadullah5171
    @mohammadasadullah5171 3 ปีที่แล้ว

    Can You send me the excel sheet of zangh

    • @genomewidestudy
      @genomewidestudy  3 ปีที่แล้ว

      zangh?

    • @mohammadasadullah5171
      @mohammadasadullah5171 3 ปีที่แล้ว +1

      @@genomewidestudy sorry boss, it was mistake. I need ling zhang excel sheet

    • @karammostafa1595
      @karammostafa1595 3 ปีที่แล้ว

      @@mohammadasadullah5171 If you still do not get this file send me your e-mail

    • @mohammadasadullah5171
      @mohammadasadullah5171 3 ปีที่แล้ว +1

      @@karammostafa1595 maullah09@gmail.com

    • @zhiyuanliu1840
      @zhiyuanliu1840 3 ปีที่แล้ว +1

      @@karammostafa1595 May I also get one? My email is zhiyuan.liu@ttu.edu Thank you!

  • @MaryamRiaz-e8g
    @MaryamRiaz-e8g 9 วันที่ผ่านมา

    For insects also plant care use for cis trans regulatory element?

  • @ribalmasri9415
    @ribalmasri9415 3 ปีที่แล้ว

    Please help doctor: in basic biosequence view, i am not getting anything after pressing start !!! what is the problem ?? thank you

    • @genomewidestudy
      @genomewidestudy  3 ปีที่แล้ว +1

      Scroll the window left right up down...

    • @ribalmasri9415
      @ribalmasri9415 3 ปีที่แล้ว

      @@genomewidestudy thank you so much doctor mashallah .. keep going.

    • @anuradhapandey8492
      @anuradhapandey8492 3 ปีที่แล้ว

      @@ribalmasri9415 even I am facing the same problem, ... Can u you please tell how u resolved it?

  • @subassreeanantharaman7927
    @subassreeanantharaman7927 2 หลายเดือนก่อน +1

    sir i have submit all datas in tb tool for visualising cis reg elements, the picture is not coming. what to do

    • @genomewidestudy
      @genomewidestudy  หลายเดือนก่อน +1

      Problem in input files, please carefully made the input file and follow the each step