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.
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?
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
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)
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?
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?
@@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 🆗 ?
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.
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?
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
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.
Dr sab I really appreciate your efforts because this video is very clear to understand.
Thanks for like and comment.
Some times TBtools visualization result shows cis elements are outside the line of gene. How can I solve this problem? Please help me sir.
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.
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?
Gene Names in length file and in element file must be same. Check the gene names
Hlo sir
Can you please make a video on SDPpred tools to determine the specificity determining position in protein
Tnks in advance
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
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)
Stress responsive
@genome Wide Study How can we show the position of cis elements in positive or negative strands?
You get the position of cis element in the data from PlantCARE. You can use that data to show the position
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?
Follow the video and input method step by step..
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?
Try to Open with
now done@@genomewidestudy
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.
Follow each step, don't skip the video. then you will solve your problem
For insects also plant care use for cis trans regulatory element?
Sir what about those CREs which have no description about it functions like unbamed 1 , 4 etc. Can we exclude those
You can exclude in the figure but must keep in the table..
@@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 🆗 ?
Yes.. Its good
@@genomewidestudy Tnkq sir for ua support
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?
yes, you can use it for other gene families as well.
Go to the supplementary data of the paper, then download the required file
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.
carefully check your data file, there must be missing of > sign with some IDs
Please help doctor: in basic biosequence view, i am not getting anything after pressing start !!! what is the problem ?? thank you
me too
Hello, I have failed to install TBtools software on my MacBook Pro. Do you know of any possible solution for this?
Download the related version, then install
Video about how to download and install tbtool
has been uploaded. I think you will get help from it.
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?
Upstream.. Because that upstream means, genes upstream, not the strand.
@@genomewidestudy thank you :))
How to make cis elements graphics with multiple gene in tbtools....?
It is already described within the video, Please watch complete video, you will find your answer. Thanks
Good veng doc
How about trans-regulatory elements.....are they also present in the promoter regions and what are their functions ?
I think literature is full of such type of information. Any how I will upload the video soon on this topic. Thanks for comment
@@genomewidestudy tnkq
Plz upload the video soon
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
Gene name in both files must be same and don't use the space bar to separate two words or figures. Use Tab
Great presentation
Glad you liked it
Nice presentation
Thanks, So nice of you
Great tutorial.....
Is there any script or command line tool to extract or download upstream/downstream regions ?
I will try to find
After setting both files on tb tool , and clicking on start ...Debung log appears . How to solve it?
Tbtool did not recognize the space between two figures or words, so use tab. there must be a space. So check your input file
@@genomewidestudyok
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.
May be your sequence have other than ATCG bases, like N or other. Check the sequence
when i press start it is showing "debug log" why this is happening?
at which step?
Informative
Thanks
Informative..
Thanks for comment.
This tool is not working, what ever I do
try to use VPN
thank you sir
So nice of you
Good
So nice
Can I get the excel sheet?
Yes you can download from the supplementary material of the manuscript, I have acknowledged in the video
Can You send me the excel sheet of zangh
zangh?
@@genomewidestudy sorry boss, it was mistake. I need ling zhang excel sheet
@@mohammadasadullah5171 If you still do not get this file send me your e-mail
@@karammostafa1595 maullah09@gmail.com
@@karammostafa1595 May I also get one? My email is zhiyuan.liu@ttu.edu Thank you!
For insects also plant care use for cis trans regulatory element?
Please help doctor: in basic biosequence view, i am not getting anything after pressing start !!! what is the problem ?? thank you
Scroll the window left right up down...
@@genomewidestudy thank you so much doctor mashallah .. keep going.
@@ribalmasri9415 even I am facing the same problem, ... Can u you please tell how u resolved it?
sir i have submit all datas in tb tool for visualising cis reg elements, the picture is not coming. what to do
Problem in input files, please carefully made the input file and follow the each step