Hi Asif, why do you use paired data t student test? Are the treatments applied to the same individuals that were control before? I am trying to use these methology in another kind of study but I need to be sure in this aspect. Because we have not paired data, measures in controls and treatments are taken in different samples.
@depthinnature6 сағат бұрын
Could you please teach it from the beginning? what is the format of the file and what data needs to be uploaded while drawing a phylogenetic tree. Thanks.
@asifmolbio6 сағат бұрын
How to perform Phylogenetic analysis using MEGA 11 software kzbin.info/www/bejne/jZecmZyAn92Bfpo
@asifmolbio6 сағат бұрын
How to construct colorful Phylogenetic tree using iTOL kzbin.info/www/bejne/foXcY4FojKqJf7s
@asifmolbio6 сағат бұрын
Watch these two videos you will understand completely
@GeneticsResearch-r2x11 сағат бұрын
Sir, for the figure at 14:30, is there any site that can generate it, or should it be created manually by illustrating the gene structure and its links with orthologs and paralogs?
@adekunleajiboye124423 сағат бұрын
Hi. Im performing volcano plots on sr plots. I am only using the FDR p-value for my cut-offs. Can I use other parameters in the cutoff and others empty? I tried it, but not working
@asifmolbio23 сағат бұрын
Like which other parameters
@adekunleajiboye12444 сағат бұрын
@@asifmolbio Thank you so much, I was able to do it
@mcmc4095Күн бұрын
Hi, do you have an english version of this lecture? Thank you!
@asifmolbioКүн бұрын
Sorry this is the only video on my channel, which is in Urdu. I will upload again with English language version
@sriswathi8426Күн бұрын
Hi Asif, can u do complete video on diversity analysis and GWAS analysis? It would be really helpful for many of us
@asifmolbioКүн бұрын
Hi, thanks for reaching out with a potential topic. I will surely record IA video on this and will upload soon
@mamarlaeeqzia4667Күн бұрын
I constructed the tree but it didn't include the first gene when color the leaves and branches
@asifmolbioКүн бұрын
@@mamarlaeeqzia4667 may be it is reordered or rearranged
@asifmolbioКүн бұрын
@@mamarlaeeqzia4667 check its position in all leaves
@mamarlaeeqzia466717 сағат бұрын
@@asifmolbio In your normal and circular tree, 2 domains are uncolored also. First one and 22. In my case, first one is uncolored, which is also first one in my Gene ID excel sheet.
@sikandarshah73262 күн бұрын
Aoa sir ap kaisay hain please suggest any scholarship only research related. In Business administration or finance or accounting for PhD. I have completed course work here in Pakistan please
@asifmolbioКүн бұрын
Wslam you can apply for chinese government scholarship. if you want to know how to process your application you can search on youtube how to apply for chinese government scholarship 2025
@safwanarif_mehmood112 күн бұрын
Respected sir kya ap cnsknowall pe b bana dyngy? Wo b aisa he hy per us main account nah ban pa raha.us main account banana seka dain.hopfully ap reply dyngy
@asifmolbio2 күн бұрын
Dear safwana, am sorry actually I never used the website you mentioned
@sonali52582 күн бұрын
sir, i have been following you and ur videos for long time and this time i need to write a review article . could you please help me in designing a review article . i have decided the topic but dont knw what specifically i need to write as i am a beginner, i even went through your video and u said that u could help those who wanted to writa a review paper . i m a newbie , and in my work i dont have any superior to guide me. please sir .
@asifmolbio2 күн бұрын
Dont worry i am here to help. What is your field of interests
@user-dr9yk6gd2s2 күн бұрын
thank you so much for these videos. its really helpful
@asifmolbio2 күн бұрын
Glad if its helpful
@nehasharma79122 күн бұрын
Suggest me some database through which by using maximum likelihood with 1000 bootstrap parameters applicable instead of mega database. As in the above explained database not even showing any type of parameter settings.
@asifmolbio2 күн бұрын
It can simple help to show already made tool to make it color and even can show branching lengths and along with bootstrap values in the form of percentage.
@asifmolbio2 күн бұрын
If you are interested in more tools you can try For phylogenetic analysis using maximum likelihood (ML) with 1000 bootstrap replicates, several databases and tools offer more advanced settings compared to the MEGA software. Here are a few options: 1. **RAxML (Randomized Axelerated Maximum Likelihood)**: - RAxML is a popular tool for ML-based phylogenetic analysis. It allows you to set various parameters, including the number of bootstrap replicates. RAxML can handle large datasets efficiently and provides detailed control over the analysis. 2. **IQ-TREE**: - IQ-TREE is another powerful tool for phylogenetic analysis using ML. It supports a wide range of substitution models and allows users to specify the number of bootstrap replicates. It also offers a fast algorithm for bootstrap analysis. 3. **PhyML (Phylogenetic Maximum Likelihood)**: - PhyML is a straightforward tool for ML phylogenetic analysis. It provides options for different substitution models and the number of bootstrap replicates. PhyML is user-friendly and integrates well with other bioinformatics tools. 4. **PAUP* (Phylogenetic Analysis Using Parsimony)**: - PAUP* offers ML analysis and is highly customizable, allowing users to specify detailed parameters, including bootstrap replicates. It is a comprehensive tool but may have a steeper learning curve compared to other software. 5. **MrBayes**: - While primarily used for Bayesian inference, MrBayes also supports ML-based methods and bootstrap analysis. It is versatile and allows extensive parameter settings. These tools typically require command-line use, offering greater flexibility and control over your analyses. They are well-suited for advanced phylogenetic studies requiring detailed parameter customization.
@dr.manzoorahmad26824 күн бұрын
Please guide how we can prepare such an excel file, can we download this file from any site like shinygo or some other website, how to get up genes and down genes???? please elaborate on this
@asifmolbio3 күн бұрын
How to calculate fold change FC, log2FC, Pvalue, Padj, Up and down regulated genes kzbin.info/www/bejne/fnmWfp-iabxojac
@asifmolbio3 күн бұрын
Here you go 👆
@dr.manzoorahmad26823 күн бұрын
@@asifmolbiothis link is not helpful to me, I am working on network pharmacology problem, mostly my work is on gene ontology, KEGG analysis, gene expression not RNA seq
@asifmolbio3 күн бұрын
@@dr.manzoorahmad2682 two ways first you get your own transcriptomic data for second option i will share another link
@asifmolbio3 күн бұрын
How to analyze public RNA-seq datasets using iDEP tool kzbin.info/www/bejne/eHqYZ35pnL6XmtU
@TaranKhan-hl7rn4 күн бұрын
Very good work. Thanks
@asifmolbio4 күн бұрын
Glad if you like it
@MatiUllah-g2n5 күн бұрын
So if we use this in our research articles, there will be no plagiarism right ?
@asifmolbio5 күн бұрын
Yes no plagiarism
@muhammadrizwansaleem5905 күн бұрын
Excellent
@asifmolbio5 күн бұрын
@@muhammadrizwansaleem590 thanks
@afreenkhan60086 күн бұрын
what is logfc value
@asifmolbio6 күн бұрын
Log fold change (log FC) is a measure used in various fields, particularly in genomics and transcriptomics, to represent the change in expression levels of genes between different conditions. It is calculated as the logarithm (typically base 2) of the fold change, which is the ratio of the expression level of a gene under one condition to its expression level under another condition. Mathematically, it is expressed as: \text{Log Fold Change (log FC)} = \log_2 \left(\frac{\text{Expression level in condition A}}{\text{Expression level in condition B}} ight) • A log FC of 1 indicates that the expression level of a gene has doubled. • A log FC of 0 indicates no change in expression. • A log FC of -1 indicates that the expression level has been halved. Using a logarithmic scale helps to manage wide ranges of fold changes and provides a more intuitive understanding of the relative changes in expression levels.
@afreenkhan60086 күн бұрын
How to add logfc value if i have only one set of data
@asifmolbio6 күн бұрын
@@afreenkhan6008 if no control you cannot calculate fc hence cannot use this plot
@afreenkhan60086 күн бұрын
@@asifmolbio can i get your email id I'll share uh my file please look once.
@addisugetahun84186 күн бұрын
Dear Dr. Asif, how are you? I have SNP data, but am troubling to prepare the input data for LD analysis, Chromosome distribution, Peak venn, Circos plot analysis in SRPLOT, so I need your help.
@asifmolbio6 күн бұрын
@@addisugetahun8418 whats error
@asifmolbio6 күн бұрын
How to avoid common errors/problems in SR plot data analysis tool? kzbin.info/www/bejne/inOWdGudZ7V5etE
@asifmolbio6 күн бұрын
Check this video if its helpful
@wizardlegend076 күн бұрын
Pls does this database work for plant related disease sir?
@asifmolbio6 күн бұрын
Sorry it doesn’t
@wizardlegend077 күн бұрын
Thanks Dr. pls is their a webtool for drawing a flowchart or figure for a review paper sir
@asifmolbio7 күн бұрын
@@wizardlegend07 biorender
@asifmolbio7 күн бұрын
@@wizardlegend07 draw.io
@asifmolbio7 күн бұрын
@@wizardlegend07 but my best choice is powerpoint
@asifmolbio7 күн бұрын
How to make a graphical abstract using powerpoint | Complete workshop kzbin.info/www/bejne/pJvVY6yBp9CWhaM
@loverofimrankhan9457 күн бұрын
Hi! Please lemme know about product size. My colleagues said it should b 200bp for qpcr but you didn't tell about this in your video. Please reply me
@asifmolbio7 күн бұрын
Yes ideally 200-250 bp but upto 400-500 is also okay
@loverofimrankhan9457 күн бұрын
What about 135pb or 150pb
@asifmolbio7 күн бұрын
@@loverofimrankhan945 still okay
@mamarlaeeqzia46677 күн бұрын
Thanks for the information. I regularly watch your videos. Currently, a masters student in China. I have identified genes through GWAS of flower color. Then i performed phylogenetic analysis, motif analysis and functional analysis of motif. What kind of other wet lab analysis can be performed?
@mamarlaeeqzia46677 күн бұрын
Now i am doing functional analysis of these genes, Transformation etc..
@asifmolbio7 күн бұрын
GWAS or characterization? Looks great can go for publication
@mamarlaeeqzia46677 күн бұрын
@@asifmolbio Genome-wide identification, Now doing function analysis, over-expression vector
@mamarlaeeqzia46677 күн бұрын
@@asifmolbio genes belong to light receptor gene family, so will check the expression under different light conditions.
@asifmolbio7 күн бұрын
Sounds good
@safwanarif_mehmood118 күн бұрын
And i thnk you should make some more videos on this.
@asifmolbio8 күн бұрын
Thanks for suggestion, i am planning
@AbdulManan-ob3xj8 күн бұрын
Thank you sir :)
@asifmolbio8 күн бұрын
Most welcome!
@AbdulManan-ob3xj8 күн бұрын
Great :) Thank you sir
@asifmolbio8 күн бұрын
So nice of you
@AbdulManan-ob3xj8 күн бұрын
Great :)
@asifmolbio8 күн бұрын
Thanks for the visit
@ShahidMahmood-m6q8 күн бұрын
how to check the animal cytology database. for example detailed protocol of the lysosome tracker experiment in macrophage cells.
@asifmolbio8 күн бұрын
To check the Animal Cytology Database for a detailed protocol like the Lysosome Tracker experiment in macrophage cells, follow these steps: ### 1. **Access the Database:** - Go to the Animal Cytology Database website or portal where it is hosted. - Log in if credentials are required. ### 2. **Search for Protocols:** - Use the search bar and type keywords such as "Lysosome Tracker," "macrophage cells," or "lysosomal staining protocol." - You can also navigate through the sections dedicated to specific cell types or experimental methods. ### 3. **Filtering and Refining Search:** - Filter your results by cell type (e.g., macrophages), assay type (e.g., fluorescence microscopy), or specific dyes like Lysosome Tracker. - Refine the search by publication date or relevance if the database allows for advanced search options. ### 4. **Accessing the Protocol:** - Once you find the relevant protocol, click on it to access the full details. - Download or save the protocol as needed. ### 5. **Using External Resources:** - If the protocol is not available in the database, consider checking other scientific protocol repositories like **Bio-protocol**, **Addgene**, or **JOVE**. - You can also search published articles on platforms like **PubMed** or **Google Scholar** for the specific experimental method. ### 6. **Contacting Database Support:** - If you are unable to locate the protocol, reach out to the database's support team or consult with colleagues who might have access to this protocol. ### General Outline for Lysosome Tracker Experiment in Macrophages: If you do not have direct access to the database and need a general overview of the experiment, here’s a simplified protocol: 1. **Cell Preparation:** - Culture macrophage cells in appropriate medium until they reach the desired confluence. 2. **Lysosome Staining:** - Incubate cells with Lysosome Tracker dye at a concentration recommended by the manufacturer (e.g., 50 nM to 1 µM). - Incubate for 30 minutes at 37°C. 3. **Washing:** - Wash cells gently with warm PBS to remove excess dye. 4. **Fixation (Optional):** - Fix cells with 4% paraformaldehyde for 10 minutes if live-cell imaging is not required. 5. **Imaging:** - Observe the stained cells using a fluorescence microscope with the appropriate filter set for Lysosome Tracker (typically green or red fluorescence). 6. **Analysis:** - Capture images and quantify lysosomal distribution or fluorescence intensity using image analysis software. If you need the exact protocol, it’s best to refer to the Animal Cytology Database or other specialized resources.
@user-ri8fh6qh3o8 күн бұрын
its works really well
@asifmolbio8 күн бұрын
Yes it does
@khushbookumari-17528 күн бұрын
Sir mere Transcriptome and metabolics dono ki file aayi analysis karne ke but mujhe samajh nhi aa raha h kaise start kru please help me sir.
@asifmolbio8 күн бұрын
A bioinformatics guide to Metabolomic Data analysis interpretation kzbin.info/www/bejne/gWPUiqiCaNFjeZY
@asifmolbio8 күн бұрын
here is a video of metabolome
@asifmolbio8 күн бұрын
if still videos are not helpful, one to one live session can be booked at forms.gle/aEVUtAzrbSHxeN659
@khushbookumari-17528 күн бұрын
Sir jo mujhe Transcriptome ke sath file milta hai jisme heatmap, kegg and kuch or relationship wale file dete hai oo kya jo hmare samples ke data hote hai ya different.
@asifmolbio8 күн бұрын
hamry hi samples ka data hota hai yeh
@mdamanat36119 күн бұрын
Dear Sir, i like your video so much. Kindly make a video of PCA analysis from the protein-ligand complex (Got by docking)
@asifmolbio9 күн бұрын
How to draw a principal component analysis (PCA) plot easily? kzbin.info/www/bejne/g4rMdWN4n96hicU
@asifmolbio9 күн бұрын
Dear MD Manat, Here is video for PCA analysis
@asifmolbio9 күн бұрын
For docking i will upload soon
@mdamanat36118 күн бұрын
Thank you sir. Hopefully you will make the video soon. Eagerly waiting for this.
@subekadass26689 күн бұрын
Sir can you put a video on prognostic model development in cancer
@asifmolbio9 күн бұрын
Dear Subeka Dass, i have started a project to explore about cancer. Many more detailed videos will be posted. Thanks for suggesting this topic
@DB-kv3wu9 күн бұрын
Interesting!
@asifmolbio9 күн бұрын
Yes really interesting
@monishamitra1519 күн бұрын
Is it free like SR plot
@asifmolbio9 күн бұрын
@@monishamitra151 yes its free
@zohaibatif40089 күн бұрын
Wow Top-notch variety of plots. Sir your explanation very crystal clear in every video. Thank you
@asifmolbio9 күн бұрын
Thanks Zohaib, stay in touch
@HarshNegi-f6p9 күн бұрын
Best video to understand phylogenetic tree
@asifmolbio9 күн бұрын
@@HarshNegi-f6p Glad if its helpful
@zohaibatif40089 күн бұрын
Thank you so much sir. Always wait for your videos to get some cool tool for presentation of data in good manner. Allah bless you more.. Ameen
@asifmolbio9 күн бұрын
Thanks Zohaib, May Allah bless you too
@AbdulManan-ob3xj10 күн бұрын
Really informative Thank you Sir! :)
@asifmolbio10 күн бұрын
Glad if it is helpful
@jagdishchand932110 күн бұрын
Your information are very helpful... Thank You soo much sir
@asifmolbio10 күн бұрын
Thanks and glad if its helpful
@strange593512 күн бұрын
thankyou soo much sir, i am working on single cell rna kindly make some video on it.
@asifmolbio12 күн бұрын
Sure, thanks for suggesting this topic
@asifmolbio12 күн бұрын
I will record
@Beautifullife718912 күн бұрын
Sir , Demo of metaboanalyst with one example
@asifmolbio12 күн бұрын
Sure, thanks for suggesting a potential topic.
@arsalan800113 күн бұрын
That's a lot of efforts
@asifmolbio13 күн бұрын
You’re welcome
@BrendaAtsieno13 күн бұрын
I can see
@asifmolbio13 күн бұрын
:p
@muhammadsulaiman602314 күн бұрын
Highly recommended channel
@asifmolbio14 күн бұрын
Thanks
@muhammadsulaiman602314 күн бұрын
The first ever high recommended biology channel in mother language... highly recommend
@asifmolbio14 күн бұрын
Thanks
@AmanUllah-tk6wt14 күн бұрын
What are the following column headings abbreviations of? sdgoi: sdendo: deltact:
@asifmolbio14 күн бұрын
Standard deviation of gene of interest Standard deviation of endogenous (house keeping) gene Delta critical threshold
@TajwarSultana-d1o14 күн бұрын
Your videos are very significants for the students who don't know anything about MB. APPRECIATED
@asifmolbio14 күн бұрын
Glad if its helpful
@VINHNGUYỄNTHÀNH-m8r15 күн бұрын
Thank you sir
@asifmolbio15 күн бұрын
Welcome
@DanielOliveira-bq9cm15 күн бұрын
What should I do if the interactive screen doesn't appear?
@asifmolbio15 күн бұрын
I have also responded to you via email. Please share the code you tried and let me know if you are using Windows?