Genome Wide Study
Genome Wide Study
  • Видео 205
  • Просмотров 577 025
Sequence Extraction and Primer designing #GCRDT Part 03
In this video, we will try to learn that how we can extract the sequence of the gene and design the primer.
How to take the sequence for gene cloning?
How to extract the CDS sequence for gene cloning?
How to extract the sequence from NCBI?
How to extract the sequence from Phytozome?
How to use the tbtool to extract the sequence?
How to design the primer for gene cloning?
How to use primer3plus to design the primer for gene cloning?
Gene cloning and DNA technology
What are the GC content of the primer?
Expression data extraction: ruclips.net/video/5BQNnWada88/видео.html
Link for Primer3Plus: www.primer3plus.com/index.html
#bioinformatics
Просмотров: 241

Видео

Gene selection for Project GCRDT 02
Просмотров 2556 месяцев назад
In this video we try to learn that how we can select the genes for our research. How to select the genes for research? Why I choose this gene for my research? Why you selected this gene? Why you want to work on this gene? How you selected this gene? How to do the blast analysis? How to select the gene for gene cloning? Gene selection for recombinant dna technology? How to screen the genes? How ...
Gene cloning and Recombinant DNA technology (DCRDT) Introduction
Просмотров 2096 месяцев назад
In this series of lectures, I will guide you all the process involved in gene cloning and recombinant DNA technology. What is gene clonig? How to clone the gene? What is clone? What is genetic engineering? What is gene? How to do recombinant DNA technology? How to transfer the gene? How to clone the gene? How to select the gene for cloning and characterization? #bioinformatics #geneclonig #dna
Delta delta ct method
Просмотров 2,4 тыс.6 месяцев назад
In this video we will calculate the qRT PCR data through delta delta ct method. What is delta delat ct method? How to calculate the qRT PCR data? How to calculate the expression of gene through delta delta ct method? How to calculate the expression of the gene? What is ct value? qRT PCR calculation for beginners delta delta Ct method in Excel Relative fold Change of rt pcr in excel How to perfo...
Sequence manipulation
Просмотров 1406 месяцев назад
In this video we will manipulate the sequence according to the requirement. How to manipulate the sequence? How to reverse the sequence? How to get the reverse sequence of the gene? How to get the reverse complement sequence of the gene? How to convert the CDS sequence into RNA sequence? How to make the sequence in upper case? How to arrange the sequence in one line? How to remove the sequence?...
Primer designing and validation #ePCR
Просмотров 2426 месяцев назад
In this video we will validate our primers for cloning or qPCR. How to design the primer? What is epcr? What is amplifix? How to design the primer with amplifix? What is in sillico pcr? How to validate the primers for in sillico pcr? How to validate the primer for pcr? How to validate primer for qPCR? How to validate primer for gene cloning? What are the qualities of the primers? How much the s...
How to add scale bar in confocal image
Просмотров 2346 месяцев назад
In this video we will learn that how we can add the scale bar in our image. How to add the scale bar in the image? How add scale bar in confocal generated image? How to add scale bar in camera generated image? What is scale bar? How we add scale bar? Why we add scale bar in our image? How to add camera photo scale bar? How to set the unit in the scale bar? What are the units of the image? How t...
Primer validation for PCR in sillico PCR
Просмотров 2527 месяцев назад
In this video we will validate our primers for cloning or qPCR. How to design the primer? What is in sillico pcr? How to validate the primer for pcr? How to validate primer for qPCR? How to validate primer for gene cloning? What are the qualities of the primers? How much the size of the primer? What are the GC contents of the PCR? What is the tempertature difference between farward and Reverse ...
How to add scale bar in camera photo
Просмотров 2537 месяцев назад
In this video we will learn that how we can add the scale bar in our image. How to add the scale bar in the image? What is scale bar? How we add scale bar? Why we add scale bar in our image? How to add camera photo scale bar? How to set the unit in the scale bar? What are the units of the image? How to show the image unit? How to optimize the unit of the scale bar? How to add scale bar in micro...
How to calculate the area of circle, irregular square images
Просмотров 2767 месяцев назад
In this video we will use the ImageJ to calculate the area of any type of image. How to calculate the area of circular image? How to calculate the area of regular image? How to calculate the area of irregular image? How to calculate the area of any shape of image? How to measure surface area? How to set the scale in image? How to run the imageJ? How to measure in the imageJ? How to find average...
Protein Alignment
Просмотров 1,2 тыс.7 месяцев назад
How to do protein sequence alignment? How to align the protein sequence? Easy way to sequence alignment How to make colorful sequence alignment? Sequence alignment in tbtools How to do alignment in muscle wrapper Muscle wrapper alignment How to remove the gaps in the alignment? Sequence alignment in one click #proteinsequence #alignment #genome
Genome wide analysis Genome wide study 2024 Part 15
Просмотров 9007 месяцев назад
In this video I will describe that what type of other analysis you can include in the GWA of your protein family. The link of each analysis related video is as under Differential Expression Genes: ruclips.net/video/5BQNnWada88/видео.html Heatmap video 1: ruclips.net/video/RDzYDHApB8s/видео.html Heatmap video 2: ruclips.net/video/W9MIZPELBjo/видео.html Promoter region extraction in Bulk: ruclips...
Protein secondary structure Genome wide study 2024 Part 14
Просмотров 5477 месяцев назад
In this video we will try to find out the secondary structure of the protein and try to know its construction. How to predict the secondary structure of the protein? How to determine the alpha sheet of the protein? How to determine the Beta sheet of the protein? How to determine the coil region of the protein? What is the secondary structure prediction method? What is the protein structure? #Pr...
Protein modeling Genome wide study 2024 Part 13
Просмотров 6157 месяцев назад
Homology modeling has become a useful tool for the prediction of protein structure when only sequence data are available. Structural information is often more valuable than sequence alone for determining protein function. Homology modeling is potentially a very useful tool for the researchers. In this video, we will discuss about the protein homology, how to do the homology analysis and result ...
Gene Location on chromosome Genome wide study 2024 Part 12
Просмотров 1,2 тыс.7 месяцев назад
In this video, we will try to construct the phenogram to present the genes distribution on different chromosomes through different tools like TBTool. How to use GFF file to make gene location on chromosome? How to use tbtools to show genes on chromosome? How to make Gene ID file? How to make gene link file? How to make Gene rename file? How to make color map? How to use gene ids to make phenogr...
Ka ks values calculation through #MEGA Genome wide study 2024 Part 11
Просмотров 1,9 тыс.8 месяцев назад
Ka ks values calculation through #MEGA Genome wide study 2024 Part 11
Protein family Physical Property Genome wide study 2024 Part 10
Просмотров 8118 месяцев назад
Protein family Physical Property Genome wide study 2024 Part 10
Protein family Property Table Genome wide study 2024 Part 09
Просмотров 1,1 тыс.8 месяцев назад
Protein family Property Table Genome wide study 2024 Part 09
Domain, gene structure, motif analysis Genome wide study 2024 Part 08
Просмотров 2,2 тыс.8 месяцев назад
Domain, gene structure, motif analysis Genome wide study 2024 Part 08
Phylogenetic Tree Genome wide study 2024 Part 07
Просмотров 1,6 тыс.8 месяцев назад
Phylogenetic Tree Genome wide study 2024 Part 07
Sequence for Phylogenetic Tree part 01 Genome wide study 2024 Part 06
Просмотров 1,3 тыс.8 месяцев назад
Sequence for Phylogenetic Tree part 01 Genome wide study 2024 Part 06
Transcript alignment and selection Genome wide study 2024 Part 05
Просмотров 1,1 тыс.8 месяцев назад
Transcript alignment and selection Genome wide study 2024 Part 05
Blast analysis and Domain confirmation Genome wide study 2024 Part 04
Просмотров 2,3 тыс.8 месяцев назад
Blast analysis and Domain confirmation Genome wide study 2024 Part 04
Query Protein Genome wide study 2024 Part 03
Просмотров 2 тыс.8 месяцев назад
Query Protein Genome wide study 2024 Part 03
Protein family selection and Data extraction Genome wide study 2024 Part 02
Просмотров 2,2 тыс.8 месяцев назад
Protein family selection and Data extraction Genome wide study 2024 Part 02
Introduction Genome wide study 2024 Part 01
Просмотров 2,7 тыс.8 месяцев назад
Introduction Genome wide study 2024 Part 01
EditGPT AI tool to improve your research write up
Просмотров 4828 месяцев назад
EditGPT AI tool to improve your research write up
AI tool to make graph and analysis Chatgpt
Просмотров 4508 месяцев назад
AI tool to make graph and analysis Chatgpt
text to fasta file #genomewidestudy
Просмотров 1,6 тыс.8 месяцев назад
text to fasta file #genomewidestudy
Phylogenetic Specie Tree #genomewidestudy
Просмотров 4008 месяцев назад
Phylogenetic Specie Tree #genomewidestudy

Комментарии

  • @RohitSharma-z3z5k
    @RohitSharma-z3z5k День назад

    Sir what we will do if we get the protein family membership then what I should write in description

  • @wafairamkhan3399
    @wafairamkhan3399 День назад

    Hello, i need your help. How can i contact you?

  • @shikhabharti4091
    @shikhabharti4091 4 дня назад

    How do we get bootsrap values for this tree?

  • @divyasingh7518
    @divyasingh7518 10 дней назад

    sir the link you provided is not opening and in google if i am opening kaks calculation tool the box in which sequences to be upload is not showing only desription about kaks is showing

  • @DewiSaroh-d3h
    @DewiSaroh-d3h 14 дней назад

    Hai, can you help me to share the link download? I followed your link but it didn't work. Thank you.

  • @jawadali-i6v
    @jawadali-i6v 16 дней назад

    AOA. Thank for efforts. Sir while I perform the Promoter Analysis the Cis Elements, they are not just located on lines but are dispersed over the Whole page. I want to know why is it happening? I shall be waiting for your Response. Thanks in Advance!

  • @marziehdavoudi4004
    @marziehdavoudi4004 23 дня назад

    I think when the Final file is empty it means non of the GO terms are significant. so those that you chose from each excel file they all had P-value of 1 and they are not significant. do you think that we can make our GO bar graph with non significant GO terms?

  • @mahfujahmedpranto8969
    @mahfujahmedpranto8969 23 дня назад

    "When I performed a phylogenetic analysis of different species in MEGA XI for a gene family, it kept crashing. What might be the reasons for this? Is there any criterion for selecting other species for my query protein in phylogenetic tree?"

  • @naushensarwar9355
    @naushensarwar9355 Месяц назад

    Sir here some species or plant genes are not found😢 then how to download promoter sequence for those plants?? Kindly guide us

    • @genomewidestudy
      @genomewidestudy 27 дней назад

      NCBI, find video with key words "genome wide study sequence download from NCBI"

  • @JaveriaSeyal
    @JaveriaSeyal Месяц назад

    Is it possible to have enrichment value 1 for all genes ?

  • @JaveriaSeyal
    @JaveriaSeyal Месяц назад

    I have finished the KEGG analysis and got the result files and have all the Columns as you have. So I try to do the enrichment bar plot but when I upload the files and press start, it just shows a blank page. Can you help me with this problems?

  • @lovelyking9197
    @lovelyking9197 Месяц назад

    Can you please recommend any papers in which the methodology for calculating ka/ks values using a phylogenetic tree has been explained?

  • @sohailahmed8716
    @sohailahmed8716 Месяц назад

    Dear as I have made a heatmap graph of metabolites 69 but in visualization it's only showing only 38... Can you guide how to plot on all 69... Pls

  • @smartbiology123
    @smartbiology123 Месяц назад

    AoA sir I'm doing same work on HMA, during motif analysis by genome jp, the motif finder didn't show the HMA motif in HMA 1 & 4. In U'r study their is missing if u check, what's the problem and how to fix it?

  • @zxzhao5
    @zxzhao5 Месяц назад

    Hi, I have a problem when I tried to highlighted some gene in dual systeny plot. I saw you copy and paste a list of genes from excel to the field "Gene list for highlight". What gene ID you use? What format of gene ID I have to follow?

  • @SherAli-g7o
    @SherAli-g7o Месяц назад

    Very informative sir Thank you sir

  • @mecca_heart
    @mecca_heart Месяц назад

    Informative, engaging, and utterly captivating🙌🏻♥️

  • @ZubairMalik-i9z
    @ZubairMalik-i9z Месяц назад

    Informative

  • @NadiaYounas-f6h
    @NadiaYounas-f6h Месяц назад

    Very Informative

  • @nasirkorai5569
    @nasirkorai5569 Месяц назад

    Very informative

  • @intrustedvideo53
    @intrustedvideo53 Месяц назад

    Very informative

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Thanks, keep watching, sharing and comment

  • @Irsa-w9s
    @Irsa-w9s Месяц назад

    Very informative

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Thanks, keep watching, sharing and comment

  • @RanaShahzaib-b6b
    @RanaShahzaib-b6b Месяц назад

    𝐼𝑛𝑓𝑜𝑟𝑚𝑎𝑡𝑖𝑣𝑒

  • @AimanKareemBukhsh
    @AimanKareemBukhsh Месяц назад

    Informative

  • @umarpathologist5863
    @umarpathologist5863 Месяц назад

    please remove the noise from audio

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Thanks for the suggestion, I will try my best to improve the audio quality in the future videos.

  • @selena91-z7v
    @selena91-z7v Месяц назад

    how to calculate absolute abundance of total bacteria in my sample using qpcr

  • @muhammadramzan6009
    @muhammadramzan6009 Месяц назад

    i have done this but did not find it.

    • @genomewidestudy
      @genomewidestudy Месяц назад

      what type of msg you have got from the tbtools after completing the analysis

  • @sherzaman203
    @sherzaman203 Месяц назад

    how did you use different genes in mega tree?? how did you make an alignme nt?

    • @genomewidestudy
      @genomewidestudy Месяц назад

      If you follow the series genome wide analysis 2024, you will get the answer of all your queries.

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Any how for alignment, find and watch the video with keywords "Protein sequence alignment genome wide study"

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Any how for mega tree, find and watch the video with keywords "Phylogenetic tree genome wide study"

  • @sherzaman203
    @sherzaman203 Месяц назад

    I have 13 protein coding genes for one genome. How can i do that?? should i take sequences from references or not?

    • @genomewidestudy
      @genomewidestudy Месяц назад

      No need to take sequence from reference. Use CDS seq and follow the video steps

  • @sherzaman203
    @sherzaman203 Месяц назад

    bro how did you make phylogenetic tree? did you use only CDS sequences from one genome only?? which method did you use for phylogenetic tree? can you please guide

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Please follow the whole video Used CDS seq

    • @sherzaman203
      @sherzaman203 Месяц назад

      @genomewidestudy bro can you please share your Gmail I need help regarding it

  • @MaryamRiaz-e8g
    @MaryamRiaz-e8g Месяц назад

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

  • @MaryamRiaz-e8g
    @MaryamRiaz-e8g Месяц назад

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

  • @IsahMansur-x9t
    @IsahMansur-x9t Месяц назад

    Please Dr, kindly make a video on SNPs analysis of gene family

  • @IshaAshraf-q4u
    @IshaAshraf-q4u Месяц назад

    Sir when we work on pfam , results differ from those in video

    • @genomewidestudy
      @genomewidestudy Месяц назад

      I made the video through InterPro, Please check that with keywords "InterPro analysis Genome wide study"

  • @jawadali-i6v
    @jawadali-i6v Месяц назад

    Sir Thank you for your Work.. I am facing a problem while doing Circos analysis Chromosomes with their names are appeared inthe image while genes names and their relation is not shown. Why its happening consistently. I shall wait for your response sir. Kindly reply. Thanks

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Check your input file, please follow each step as mentioned in the video. prepare the file carefully as I shown in the video

  • @lynseed
    @lynseed Месяц назад

    Is there a way to insert the distance? Thank you for this video!

  • @prsimoibn2710
    @prsimoibn2710 Месяц назад

    Can we start from a list of gene symbols to retrieve the promoter regions?

  • @sureshkumar-me6ri
    @sureshkumar-me6ri Месяц назад

    Pl make it clear by saying target gene and control gene. .not clear what you are talking

  • @allahissufficient2769
    @allahissufficient2769 Месяц назад

    If organisms is not on pytozome then??

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Then use NCBI or ensemble or related organism database

    • @genomewidestudy
      @genomewidestudy Месяц назад

      you can find the related video with keywords "Genome data from NCBI genome wide study"

  • @panizdarmani7411
    @panizdarmani7411 Месяц назад

    hi . i did all the things you said. the difference is i see no color line between my genes. why?

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Carefully prepare the input file, don't use space bar, use tab to make space between two digits or words

  • @nimra7354
    @nimra7354 2 месяца назад

    Sor why the 5 chromosomes of arabidopsis are not appeared in the result?? Kindly answer

    • @genomewidestudy
      @genomewidestudy Месяц назад

      May be it was removed from the GFF or any other file during adjustment

  • @naushensarwar9355
    @naushensarwar9355 2 месяца назад

    Sir, how to download gff,gtf, genome file for plant analysis because in phytozome my plant analysis not available, Kindly guide us sir

    • @genomewidestudy
      @genomewidestudy Месяц назад

      Then use NCBI or ensemble or related organism database

    • @genomewidestudy
      @genomewidestudy Месяц назад

      you can find the related video with keywords "Genome data from NCBI genome wide study"

  • @vikrantpanwar2007
    @vikrantpanwar2007 2 месяца назад

    Sir it is not working in India

  • @archuprincess5704
    @archuprincess5704 2 месяца назад

    I was following each step, suddenly TB tools ? How to get that ?

  • @archuprincess5704
    @archuprincess5704 2 месяца назад

    How to get TB tool ?

    • @genomewidestudy
      @genomewidestudy Месяц назад

      you can find the related video with keywords "how to download tbtools genome wide study"

  • @vikrantpanwar2007
    @vikrantpanwar2007 2 месяца назад

    Sir this software link is not working now.

    • @vikrantpanwar2007
      @vikrantpanwar2007 2 месяца назад

      How can we continue it

    • @genomewidestudy
      @genomewidestudy 2 месяца назад

      I have made four videos about ka ks values calculation. In these four videos, I told 4 different methods. If one did not work, you can apply next.

    • @genomewidestudy
      @genomewidestudy 2 месяца назад

      Almost for all analysis, I have made two to three videos of different methods.

    • @vikrantpanwar2007
      @vikrantpanwar2007 2 месяца назад

      Thank you sir

  • @ajlectures7101
    @ajlectures7101 2 месяца назад

    ❤ great work

  • @ajlectures7101
    @ajlectures7101 2 месяца назад

    Simple and impressive

  • @ajlectures7101
    @ajlectures7101 2 месяца назад

    Wonderful work

  • @panizdarmani7411
    @panizdarmani7411 2 месяца назад

    hello dr. i have 8 genes of ARF in parvula that they have same gene id . why ? what's the problem ? i get them from blast