Good mrng sir How we excluded PSEUDOGENES among the list of protein we identified......eventhough some of them do have domain of particular protein and also have motif as well of particular protein interested but either this have protein sequences started with Tryptophan not with Methionine OR some of them doesn't have particular protein others physicochemical property and structure property.....so can we excluded those ?
In case if all the genes don't contain HSP70 so the genes which don't contain HSP70 we have to discard them because we don't have concerned with them so how we will delete these gene ?
Hello, regarding the start and end point, Why did you count 12 the back and not continue from 1 and stop at 618, as indicate on the pfam website? I hope to hear from you. Thank you.
According to PFAM, our domain region start from 12th amino acid of the query sequence and ends at 618th amino acid. thats why we have selected this region.
Hello sir, thank you for the informative lectures. I have a question that is it necessary to remove redundant protein sequences? Some papers mentioned that the redundant sequences were removed. Thank you for your attention!
@@genomewidestudy Sorry for bothering you again, sir! I’m wondering that is it considered as redundancy if two protein sequences only have one different amino acid residue (but they are encoded by two genes and have different chromosome locations?) I'm thankful for your help.
@@Muhammadagric Already video is present about domain analysis, search with key words "Domain analysis genome wide study" you will find the related video
Salam. Sir, I have a question, if a protein contains many domains. for example Knotted1-like Homeobox protein contains four domains.... KNOX1, KNOX2, ELK, and HOX... how can we further process the extraction?
you check the related domain of family in the gene. If it contains that domain then it is the part of the family. Some family have more than 1 domain in theor members. First confirm that your studied family have how many domains in their members
@@genomewidestudy Yes but which domain we need to take for further analysis??. Like If our gene family has 4 domains then how can we further process this?
@@uroosazaheer6773 if your family have 4 domains then all four domain you will take to do further analysis. better to use complete gene sequence which have all the four domains alongwith other AA
Salam, as I am working on HSF transcription factors, but I am confuse in finding query, as you used specific protein but I am working in whole family, so kindly guide how to work with that.. Thanks
AoA sir, when we search for a specific gene in Arabidopsis thaliana on NCBI then we find many genes related to our search. on what basis we should select the one for the next steps?
Salam. Sir, Can you please make a short video, how to add in cart in new Phytozome database website... I have blast the gene but there is no option Add cart and view cart..... Thank you.... actually they have changed the settings.....
Salam Sir! Quite useful and informative lecture. Can you please guide me that should we include all transcripts of a gene for further analysis or only consider primary transcript for genome wide study of a gene?
Please first read the literature that microRNA interact with which stage of the gene, either before translation, or after translation.. Then you will be clear that which analysis will do..
E-values means to provide convincing evidence that two sequences are homologs or how much similarity is present between the query and retrieved sequences
Thanks for your comment. If you need some specific type of analysis, I will also make the video on it. anyhow, you will see the videos of this series in the coming week.
@@genomewidestudy wow that cools. Making a circos with Tbtools can also be a good analysis to explore. Thanks for your time. You are helping a lot of student and people.
![Felix "Unfair" | [Stray Kids : SKZ-PLAYER]](http://i.ytimg.com/vi/Oswujxm2Ag0/mqdefault.jpg)
MashALLAH, better voice quality in comparison to earlier video. 👍🏼👍🏼👍🏼
Good mrng sir
How we excluded PSEUDOGENES among the list of protein we identified......eventhough some of them do have domain of particular protein and also have motif as well of particular protein interested but either this have protein sequences started with Tryptophan not with Methionine OR some of them doesn't have particular protein others physicochemical property and structure property.....so can we excluded those ?
Now it is Better Keep it up superb
Can you explain any other route for data extraction of plant species not present on phytozome?
You can find the videos in the list in which I have explained the other sources to extract the data
Can you explain how to use The hidden Markov model (HMM) profile and subsequently exploited for the identification gene family?
Nice work, simple explaination... easy to understand
sir the phtyozome is a species-limited tool (like coconut plant info is not available), what we can do in this case? kindly guide me.
You can watch the video with title
How to find gene information from NCBI gene ID | Transcript ID | Gene name from NCBI
Also follow this video
How to find the GFF GTF file and sequence data of different organisms from NCBI
@@genomewidestudy thanks for the quick response..
Sir, i have problem while using Phytozome 13 new vwrsion, i can,t add chart option its not working ? plz guide me
have you logged in?
@@genomewidestudy Yes,sir issue solved thanks, one more question why we select last 12 amino acids in pfam sequence little bit conufusion ?
Sir when we work on pfam , results differ from those in video
I made the video through InterPro, Please check that with keywords "InterPro analysis Genome wide study"
In case if all the genes don't contain HSP70 so the genes which don't contain HSP70 we have to discard them because we don't have concerned with them so how we will delete these gene ?
Simply select and press delete..
Hello, regarding the start and end point,
Why did you count 12 the back and not continue from 1 and stop at 618, as indicate on the pfam website? I hope to hear from you. Thank you.
According to PFAM, our domain region start from 12th amino acid of the query sequence and ends at 618th amino acid. thats why we have selected this region.
I understand but why did you skip the last line before counting 12? How were you able to achieve the 618 mark?
Because 618th amino acid comes before last line.
@@genomewidestudy How
@@worldamazingfood2570 You can count the amino acid..
Hello sir, thank you for the informative lectures. I have a question that is it necessary to remove redundant protein sequences? Some papers mentioned that the redundant sequences were removed. Thank you for your attention!
It is better to remove.
@@genomewidestudy Thank you very much!
@@genomewidestudy Sorry for bothering you again, sir! I’m wondering that is it considered as redundancy if two protein sequences only have one different amino acid residue (but they are encoded by two genes and have different chromosome locations?) I'm thankful for your help.
They are two gene with SNP mutation. So you must include both
@@genomewidestudy Thank you so much! :))
MashAllah very nice video
Many many thanks
Very good keep it up
Thank you so much 😀
Sir, my works is on pear fruit, but in phytozome i didn't find my specie how can i find gene sequences there? like tomato
Watch the video Entitled "How to find the GFF GTF file and sequence data of different organisms from NCBI"
Sir i have pear fruit (Pyrus pyrifolia) but i dont find my fruit in phytozmome any solution?
Please follow the video with title
How to find the GFF GTF file and sequence data of different organisms from NCBI
@@genomewidestudy Sir i have GFF GTF file but i dont understand how can i do domain anlysis
@@Muhammadagric Use Protein file to do domain analysis
@@Muhammadagric Already video is present about domain analysis, search with key words "Domain analysis genome wide study" you will find the related video
Salam. Sir, I have a question, if a protein contains many domains. for example Knotted1-like Homeobox protein contains four domains.... KNOX1, KNOX2, ELK, and HOX... how can we further process the extraction?
you check the related domain of family in the gene. If it contains that domain then it is the part of the family.
Some family have more than 1 domain in theor members. First confirm that your studied family have how many domains in their members
@@genomewidestudy Yes but which domain we need to take for further analysis??. Like If our gene family has 4 domains then how can we further process this?
@@uroosazaheer6773 take the genes that have all the four domains or any one from that. Because some families have the partials genes .
@@uroosazaheer6773 there are series of lectures, So follow them step by step
@@uroosazaheer6773 if your family have 4 domains then all four domain you will take to do further analysis. better to use complete gene sequence which have all the four domains alongwith other AA
Great Work. Keep it up Dr..
there is no brassica napus in phytozone, so kindly tell me what to do, there is problem on pfam no data donload, guide me what to do????
Follow this video
How to find the GFF GTF file and sequence data of different organisms from NCBI
Also this one
Downloading Promoter CDS Protein Genomic sequence of a gene from NCBI
@@genomewidestudy thanks so much، let i try this ❤️
Salam, as I am working on HSF transcription factors, but I am confuse in finding query, as you used specific protein but I am working in whole family, so kindly guide how to work with that.. Thanks
ws. you can also find the query protein of HSF, as I shown in the video to find the query protein of HSP70.
use same method except changing tha name of protein from HSP70 to HSF
AoA sir, when we search for a specific gene in Arabidopsis thaliana on NCBI then we find many genes related to our search. on what basis we should select the one for the next steps?
ws. If you want to search the gene as query, then you try to select that gene which were experimentally proved that it is belongs to this family.
Excellent explanation. Appreciated
Sir is there any video on covid virus genome
Sorry, I did not have..
really very informative
Thanks for watching
Fruitful one
Thanks for watching. Appreciated
Informative 👍
Salam. Sir, Can you please make a short video, how to add in cart in new Phytozome database website... I have blast the gene but there is no option Add cart and view cart..... Thank you.... actually they have changed the settings.....
Phytozome v13 } How to use Phytozome v13 | CDS Genome Protein Sequence from Phytozome V13
Here is video..
@@genomewidestudy Thank you very much
Nice video..
Salam Sir! Quite useful and informative lecture. Can you please guide me that should we include all transcripts of a gene for further analysis or only consider primary transcript for genome wide study of a gene?
primary.transcript
@@genomewidestudy thank you for response :)
Sir is there any tool to see the interaction between long non coding rna or mirna or mRNA with the heat shock protein?
Yes, it is.
I am making the videos.
Your related videos will be uploaded within 1_2 days.
@@genomewidestudy yes please focus on how to find the interaction between lncrna or mirna or mnra with hsp it will be really very helpful to me
RNA RNA Interaction | Download and install #VARNA Software to 2D visualization Part 01
@@genomewidestudy not rna rna... interaction between protein and rna i want to know
Please first read the literature that microRNA interact with which stage of the gene, either before translation, or after translation.. Then you will be clear that which analysis will do..
wel explained. Great work
Glad you liked it
please sir upload video on phytozome V13 by targeting RNA helicase in wheat genome
Phytozome v13 } How to use Phytozome v13 | CDS Genome Protein Sequence from Phytozome V13
Here is your required Video
What is e value 10-5? Please help me
E-values means to provide convincing evidence that two sequences are homologs or how much similarity is present between the query and retrieved sequences
@@genomewidestudy Thank you. Your videoes help me a lot
Very creative
Thanks for watching. Appreciated
Great
excellent explication, thanks videos
Glad you liked it
@@genomewidestudy Please help me with TbTools, I get an error exactly a black screen, I was doing the motifs and out of nowhere this happened.
excellent
Explain 6.39 sec moment of vedio
What it was? write your Question
we are expecting your next upload
Soon
@@genomewidestudy ok thanks. Can't wait.
Thanks for your comment. If you need some specific type of analysis, I will also make the video on it. anyhow, you will see the videos of this series in the coming week.
@@genomewidestudy wow that cools. Making a circos with Tbtools can also be a good analysis to explore. Thanks for your time. You are helping a lot of student and people.
Very well explained