Dr. Muhammad Naveed
Dr. Muhammad Naveed
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Genome Assembly & Annotations | GenMark | BV-BRC | PATRIC| WGS-2 | Lecture 424 | Dr. Muhammad Naveed
Genome Assembly & Annotations by GenMark and BV-BRC PATRIC
GenMark: opal.biology.gatech.edu/GeneMark/
BV-BRC: www.bv-brc.org/view/Taxonomy/1457300#view_tab=overview
Genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. Here are the general steps for bacterial genome annotation:
1. Sequencing:
Obtain the bacterial DNA sequence using sequencing technologies such as Illumina, PacBio, or Oxford Nanopore.
2.Preprocessing:
Quality control of the raw sequence data using tools like FastQC.
Trimming and filtering low-quality reads using tools like Trimmomatic or Cutadapt.
3. Genome Assembly:
Assemble the reads into contigs using assemblers like SPAdes, Velvet, or Canu. Scaffold the contigs into a complete genome using tools like SSPACE or using long-read data.
4. Gene Prediction:
Identify gene locations using ab initio prediction tools such as Prodigal, Glimmer, or GeneMark. Use homology-based methods by comparing the genome to known genes in databases using tools like BLAST.
MetaGenMark:
Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes
Novel prokaryotic genomic sequences can be analyzed by the self-training software tool GeneMarkS-2 (sequences longer than 50 Kb). For some species pre-trained model parameters are ready and available through the GeneMark.hmm. Metagenomic sequences and individual short sequences (sequences 50 kb) can be analyzed by MetaGeneMark.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the Year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology, Nano-informatics and vaccine designing, and Drug designing against infectious diseases. He has supervised 90 MSc. and 80 MPhil. & 02 Ph.D. students. He has published 172 Research articles with 1246 impact factors, 9560 citations, 01 book, 06 book chapters, and filed 05 Patents. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
Contact links:
1. Official website: ucp.edu.pk/member/dr-muhammad-naveed/
2. Facebook: drmuhammadnaveed22
3. LinkedIn: www.linkedin.com/in/dr-muhammad-naveed-7324b534/?originalSubdomain=pk
4. Instagram: prof.dr.naveed
5. Google Scholar: scholar.google.com/citations?user=fuEwn1cAAAAJ&hl=en
6. ResearchGate: www.researchgate.net/profile/Muhammad-Naveed-59
7. Twitter: naveedqau
#wgs #genome #annotations #bioinformatics #drmuhammadnaveed
มุมมอง: 247

วีดีโอ

Genome Sequence Retrieval, Assembly & Quality analysis | WGS-1 | Lecture 423 | Dr. Muhammad Naveed
มุมมอง 47814 วันที่ผ่านมา
Genome Sequence Retrieval, Assembly & Quality analysis (NCBI): Example link: www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/ Genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. Here are the general steps for bacterial genome annotation: 1. Sequencing: Obtain the bacterial DNA sequence using s...
Whole Genome Sequence (WGS) analysis | Overview Bacterial Genome | Lecture 422 | Dr. Muhammad Naveed
มุมมอง 93721 วันที่ผ่านมา
Whole Genome Sequence (WGS) annotation: Series overview Genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. Here are the general steps for bacterial genome annotation: 1. Sequencing: Obtain the bacterial DNA sequence using sequencing technologies such as Illumina, PacBio, or Oxford Nanopore. 2.Prep...
Cambridge University Scholarships | MS & PhD | Lecture 168 | Dr. Muhammad Naveed
มุมมอง 710หลายเดือนก่อน
Gates Cambridge Scholarships (Complete application process): Weblink: www.gatescambridge.org/programme/the-scholarship/ Apply online at: www.gatescambridge.org/apply/how-to-apply/ Application link: apply.postgraduate.study.cam.ac.uk/applicant/login?dswid=-7585 Useful Links: 1. CV Template: th-cam.com/video/GdhC7o9fHpQ/w-d-xo.html 2. Motivational Letter: th-cam.com/video/VixhSipDRRU/w-d-xo.html ...
University of Melbourne, Australia Scholarships | MS & PhD | Lecture 167 | Dr. Muhammad Naveed
มุมมอง 753หลายเดือนก่อน
University of Melbourne, Australia Scholarships (Complete application process): Weblink: scholarships.unimelb.edu.au/awards/graduate-research-scholarships Apply online at: unimelb-web.t1cloud.com/T1SMDefault/WebApps/eStudent/SM/eApplications/ApptDtls100.aspx?r=#UM.ADM.WEB&f=#UM.EAP.APPTDTLS.WEB Application link: study.unimelb.edu.au/how-to-apply/graduate-research/international-applications/appl...
Skoltech Fully Funded Scholarships for Russia | Master program | Lecture 166 | Dr. Muhammad Naveed
มุมมอง 688หลายเดือนก่อน
Skoltech Scholarships for Russia (Complete application process): Weblink: www.skoltech.ru/en/apply/msc-programs/ Apply online at: apply.skoltech.ru/ online test link: msc.skoltech.ru/exams Useful Links: 1. CV Template: th-cam.com/video/GdhC7o9fHpQ/w-d-xo.html 2. Motivational Letter: th-cam.com/video/VixhSipDRRU/w-d-xo.html 3. Reference letter: th-cam.com/video/VE25pQeQw2c/w-d-xo.html ​Applicati...
Upgrade Your Life Model with New Skills | Lecture 1008 | Dr. Muhammad Naveed
มุมมอง 1822 หลายเดือนก่อน
Transform Your Life with Essential Skills. Unlock Success: Essential Skills to Upgrade Your Life" promises a transformative journey towards personal growth and achievement. In today's dynamic world, acquiring key skills is not just advantageous but crucial for thriving in various aspects of life. Whether it's honing communication prowess to foster meaningful relationships, mastering time manage...
Focused on Blessings and Ignore Negativity | Lecture 1007 | Dr. Muhammad Naveed
มุมมอง 1412 หลายเดือนก่อน
Focused on Blessings and Ignore Negativity | Lecture 1007 | Dr. Muhammad Naveed
Stop Comparing Yourself to Others | Motivational story | Lecture 1006 | Dr. Muhammad Naveed
มุมมอง 4022 หลายเดือนก่อน
Stop Comparing Yourself to Others | Motivational story | Lecture 1006 | Dr. Muhammad Naveed
Cancer Immune response and Immunotherapy analysis | TIMER 2:0 | Lecture 421 | Dr. Muhammad Naveed
มุมมอง 9043 หลายเดือนก่อน
Cancer Immune response and Immunotherapy analysis | TIMER 2:0 | Lecture 421 | Dr. Muhammad Naveed
Statement of Purpose (SOP) | for International Scholarships | Lecture 165 | Dr. Muhammad Naveed
มุมมอง 4123 หลายเดือนก่อน
Statement of Purpose (SOP) | for International Scholarships | Lecture 165 | Dr. Muhammad Naveed
Moroccan Govt Scholarships | Fully funded for BS, MS & PhD | Lecture 164 | Dr. Muhammad Naveed
มุมมอง 1.5K3 หลายเดือนก่อน
Moroccan Govt Scholarships | Fully funded for BS, MS & PhD | Lecture 164 | Dr. Muhammad Naveed
Cancer Genes Expression analysis | GEPIA2 | DEG Survival Analysis| Lecture 420 | Dr. Muhammad Naveed
มุมมอง 1.2K4 หลายเดือนก่อน
Cancer Genes Expression analysis | GEPIA2 | DEG Survival Analysis| Lecture 420 | Dr. Muhammad Naveed
How to find Protein Sub-cellular Localization? | WoLF PSORT & BUSCA | Lec. 419 | Dr. Muhammad Naveed
มุมมอง 5934 หลายเดือนก่อน
How to find Protein Sub-cellular Localization? | WoLF PSORT & BUSCA | Lec. 419 | Dr. Muhammad Naveed
Julius AI | Experience Future of Data Analysis | Graphs & Charts | Lecture 118 | Dr. Muhammad Naveed
มุมมอง 8264 หลายเดือนก่อน
Julius AI | Experience Future of Data Analysis | Graphs & Charts | Lecture 118 | Dr. Muhammad Naveed
SciSpace | Best AI Tool for Literature Review, Paraphrasing & AI detections | Lec. 117 | Dr. Naveed
มุมมอง 2.4K4 หลายเดือนก่อน
SciSpace | Best AI Tool for Literature Review, Paraphrasing & AI detections | Lec. 117 | Dr. Naveed
How to Design Presentations with Gamma AI | Create PPT Using AI | Lecture 116 | Dr. Muhammad Naveed
มุมมอง 2K5 หลายเดือนก่อน
How to Design Presentations with Gamma AI | Create PPT Using AI | Lecture 116 | Dr. Muhammad Naveed
Perplexity AI | The Academic Writing Choice over ChatGPT | Lecture 115 | Dr. Muhammad Naveed
มุมมอง 1.2K5 หลายเดือนก่อน
Perplexity AI | The Academic Writing Choice over ChatGPT | Lecture 115 | Dr. Muhammad Naveed
Pharmit | Pharmacophore based virtual Drug screening | Lecture 114 | Dr. Muhammad Naveed
มุมมอง 1.5K5 หลายเดือนก่อน
Pharmit | Pharmacophore based virtual Drug screening | Lecture 114 | Dr. Muhammad Naveed
Online Docking in 2 minutes | with CB-Dock2 and AutoDock Vina | Lecture 113 | Dr. Muhammad Naveed
มุมมอง 1.7K5 หลายเดือนก่อน
Online Docking in 2 minutes | with CB-Dock2 and AutoDock Vina | Lecture 113 | Dr. Muhammad Naveed
GENSCAN | Identification of gene structures in genomic DNA | Lecture 112 | Dr. Muhammad Naveed
มุมมอง 8616 หลายเดือนก่อน
GENSCAN | Identification of gene structures in genomic DNA | Lecture 112 | Dr. Muhammad Naveed
PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111 | Dr. Muhammad Naveed
มุมมอง 1.4K6 หลายเดือนก่อน
PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111 | Dr. Muhammad Naveed
University of Luxembourg Scholarships | Fully funded MS & PhD | Lecture 163 | Dr. Muhammad Naveed
มุมมอง 7K6 หลายเดือนก่อน
University of Luxembourg Scholarships | Fully funded MS & PhD | Lecture 163 | Dr. Muhammad Naveed
Chief Minister Foreign Ph.D Scholarships | PEEF Fully funded PhD | Lecture 162 | Dr. Muhammad Naveed
มุมมอง 1K7 หลายเดือนก่อน
Chief Minister Foreign Ph.D Scholarships | PEEF Fully funded PhD | Lecture 162 | Dr. Muhammad Naveed
Turkiye Burslari scholarships | Fully funded for BS, MS & PhD | Lecture 161 | Dr. Muhammad Naveed
มุมมอง 4K7 หลายเดือนก่อน
Turkiye Burslari scholarships | Fully funded for BS, MS & PhD | Lecture 161 | Dr. Muhammad Naveed
PhD Indigenous Scholarship program of HEC 2024 | Complete Process| Lecture 160| Dr. Muhammad Naveed
มุมมอง 6K7 หลายเดือนก่อน
PhD Indigenous Scholarship program of HEC 2024 | Complete Process| Lecture 160| Dr. Muhammad Naveed
Post Translational Modifications (PTMs) | Complete Process | Lecture 13 | Dr. Muhammad Naveed
มุมมอง 2.3K7 หลายเดือนก่อน
Post Translational Modifications (PTMs) | Complete Process | Lecture 13 | Dr. Muhammad Naveed
Translation | Protein Synthesis | Complete Process | tRNA | rRNA| Lecture 12 | Dr. Muhammad Naveed
มุมมอง 5137 หลายเดือนก่อน
Translation | Protein Synthesis | Complete Process | tRNA | rRNA| Lecture 12 | Dr. Muhammad Naveed
Post-Transcriptional Modifications | Capping | Splicing | Tailing | Lecture 11 | Dr. Muhammad Naveed
มุมมอง 6367 หลายเดือนก่อน
Post-Transcriptional Modifications | Capping | Splicing | Tailing | Lecture 11 | Dr. Muhammad Naveed
Transcription | RNA Synthesis | DNA to RNA complete process | Lecture 10 | Dr. Muhammad Naveed
มุมมอง 5448 หลายเดือนก่อน
Transcription | RNA Synthesis | DNA to RNA complete process | Lecture 10 | Dr. Muhammad Naveed

ความคิดเห็น

  • @user-rt7nx1ji6d
    @user-rt7nx1ji6d 34 นาทีที่ผ่านมา

    Very Nice video series, i would like to ask as you found few epitopes common in all alleles, what can I do if I found all epitopes common in all alleles, if in MHC-I, I got 20000 epitopes when I sorted alleles basis and then trying to compare common epitope in all alleles, I found all are common. In such case how to pick common and proceed further for Vaxijen etc.

  • @maryamnaseer8552
    @maryamnaseer8552 3 ชั่วโมงที่ผ่านมา

    what is log.txt file. I can't get it . kindly guide

  • @Kamila-i4q
    @Kamila-i4q 4 ชั่วโมงที่ผ่านมา

    Sir agr koi 4th semester m h or us ki pichla semester ki fees refund hogyi Jo vo pay kr Chuka ha ya pir sirf Jo remaining semester rah gya h in ki tuition fee da ga kindly btay

  • @Ahmadijaz-vv4vw
    @Ahmadijaz-vv4vw 7 ชั่วโมงที่ผ่านมา

    Aoa sir can you apply for me i want to apply for MS mathematics in japan on sacholarship base

  • @saroshzahid7094
    @saroshzahid7094 8 ชั่วโมงที่ผ่านมา

    bohut shukria sir ji ...bohut behtreen video hai .bioinformatics asan kar di hai ap nay hamary lia🤲👍

  • @Nature1284
    @Nature1284 9 ชั่วโมงที่ผ่านมา

    Sir pl endnote ApA 6 and 7 ka bata de kese kary endnote me use ye styyle

  • @wishabc6465
    @wishabc6465 11 ชั่วโมงที่ผ่านมา

    usually we add results and discussion in the same section

  • @javaidrahman9458
    @javaidrahman9458 20 ชั่วโมงที่ผ่านมา

    GRE test is necessary?

  • @hirajutt2496
    @hirajutt2496 22 ชั่วโมงที่ผ่านมา

    Hat 3 kb hota hai.

  • @Saba-i7p
    @Saba-i7p วันที่ผ่านมา

    They only call short listed students? or they short list again after the interview?

  • @Saba-i7p
    @Saba-i7p วันที่ผ่านมา

    and what is the next step after the interview? and how to be successful in an interview?

  • @fazilatzahra4407
    @fazilatzahra4407 วันที่ผ่านมา

    Agr MS kaliya professor ko mail karna huwe to process kiya hai kindly thoda batya

  • @afifaisrar1318
    @afifaisrar1318 วันที่ผ่านมา

    Please let me know if we must submit the sequence and obtain the accession number first if we are using our own whole genome data?

  • @afifaisrar1318
    @afifaisrar1318 วันที่ผ่านมา

    Thank you Sir! Had been waiting on lectures regarding this analysis

  • @TahirAli-ku8mz
    @TahirAli-ku8mz 2 วันที่ผ่านมา

    ❤❤❤❤

  • @user-vy1ic3tk8b
    @user-vy1ic3tk8b 2 วันที่ผ่านมา

    what is a parent article?

  • @zshahidmughal9996
    @zshahidmughal9996 2 วันที่ผ่านมา

    Sir ,If you did graduation with no research .You are Applying for Master leading to PHD scholorship for king Abdullah university. How do I write my email than?

  • @shahidjan
    @shahidjan 3 วันที่ผ่านมา

    Asslam o laikum sir Mai Shahid Baloch khuzdar Balochistan se sir please visa k about guidelines den

  • @worldnews3717
    @worldnews3717 3 วันที่ผ่านมา

    Agar sir English achi na ho tu ??

  • @abideenff7685
    @abideenff7685 4 วันที่ผ่านมา

    Kindly Sir inform me, Is PTE acceptable for KAIST scholarship

  • @niazbahadar444
    @niazbahadar444 4 วันที่ผ่านมา

    Thank you sir Very informative lecture

  • @niazbahadar444
    @niazbahadar444 4 วันที่ผ่านมา

    Great sir very informative lecture .Sir can we use Geneious prime for annotation

  • @ProGeniusGaming454
    @ProGeniusGaming454 4 วันที่ผ่านมา

    Sir I'm facing phone number issues that's why my personal information not save kindly Tell me how can I solve this problem 😞

    • @ybgillani8777
      @ybgillani8777 4 วันที่ผ่านมา

      Please visit scholarship insight recent video. They have mentioned this issue

    • @ProGeniusGaming454
      @ProGeniusGaming454 4 วันที่ผ่านมา

      @@ybgillani8777 thanks sir ❤️

  • @iqaspirants1247
    @iqaspirants1247 4 วันที่ผ่านมา

    Excellent 👌❤

  • @mehwishfatima7651
    @mehwishfatima7651 5 วันที่ผ่านมา

    Is there anyone who can tell me how I can get proper info about HAT ?

    • @mehwishfatima7651
      @mehwishfatima7651 5 วันที่ผ่านมา

      For proper preparation of that test for English linguistics

  • @bilalbutt1374
    @bilalbutt1374 5 วันที่ผ่านมา

    😂With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the Year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology and vaccine designing, and Drug designing against infectious diseases. He has supervised 90 MSc. and 78 MPhil. & 01 Ph.D. students. He has published 150 Research articles with 1120 impact factors, 6060 citations, 01 book, 06 book chapters, and filed 05 Patents. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).

  • @nadiashoukat5189
    @nadiashoukat5189 5 วันที่ผ่านมา

    2.9 CGPA walo ka chance hai koi?

  • @sheikhatikaali131
    @sheikhatikaali131 6 วันที่ผ่านมา

    Sir ye pymol livcon use kr skte h na Ya aise dawa batao upar wale ka wasta aaapko sirr ke masse chale jaye bht preshaan ho dr bht zyadaaa 😢😢😢😢

  • @Nishithteraiya
    @Nishithteraiya 6 วันที่ผ่านมา

    prepare tutorial on how to sketch 3d structure of organometallic compounds (example-ferrocene) and their docking

  • @vidyanemade6061
    @vidyanemade6061 7 วันที่ผ่านมา

    very nicely explained

  • @noorulain1640
    @noorulain1640 7 วันที่ผ่านมา

    How can do anylysis of more than one compounds in a single run using swiss adme and how can i download these results??

  • @laibazahid7863
    @laibazahid7863 8 วันที่ผ่านมา

    My colleague published my research paper. I had done the whole work. Please help me

  • @laibazahid7863
    @laibazahid7863 8 วันที่ผ่านมา

    My colleague published my research paper. Idid the whole work on that topic. I have a complete thesis on that topic. What i do

  • @sadiaalianjum8112
    @sadiaalianjum8112 8 วันที่ผ่านมา

    Sir can you please share the video on how to know the reliability?

  • @RizvanAshraf-lp9xx
    @RizvanAshraf-lp9xx 8 วันที่ผ่านมา

    AOA. Sir Swiss target is showing this messege . Please guide. Checking the validity of the query molecule. This takes about 2 seconds. Please, wait. You are submitting molecules that are too large. Please, respect a limit of 200 characters per SMILES.

  • @rameeshaarshad6755
    @rameeshaarshad6755 9 วันที่ผ่านมา

    Thanks for accurate guidance ❤

  • @sanwalaslam107
    @sanwalaslam107 9 วันที่ผ่านมา

    If we use single strand DNA only as receptor. We have to choose protein option or another. If yes then results will be ok?

  • @jaafarbello996
    @jaafarbello996 10 วันที่ผ่านมา

    Please Sir may I get the English version of this lecture?

  • @pslgameonha6078
    @pslgameonha6078 10 วันที่ผ่านมา

    Pls sir can you tell me about methods that what are the methods that we use

  • @akshivgulati2986
    @akshivgulati2986 10 วันที่ผ่านมา

    This video is amazing!

  • @akhameed2365
    @akhameed2365 10 วันที่ผ่านมา

    Right sir❤

  • @akhameed2365
    @akhameed2365 10 วันที่ผ่านมา

    Thank u sir

  • @Strangerthingseggos124
    @Strangerthingseggos124 11 วันที่ผ่านมา

    excellent and easy to understand tutorial.

  • @noorrana2164
    @noorrana2164 11 วันที่ผ่านมา

    Great Work.

  • @asmrbymona8504
    @asmrbymona8504 11 วันที่ผ่านมา

    When I downloaded the ligand from elea3D based on the highest score and then uploaded it to the SwissTargetPredict server, it said, "You are submitting molecules that are too large. Please respect a limit of 200 characters per SMILES." What do you think I should do now? That I have all the ligands with large SMILES.

  • @BismaAbid3
    @BismaAbid3 11 วันที่ผ่านมา

    Wrong answers

  • @Peerekamil789
    @Peerekamil789 12 วันที่ผ่านมา

    I watched many videos related to Molecular Docking but your lectures are best

  • @niamatullahbaloch9358
    @niamatullahbaloch9358 12 วันที่ผ่านมา

    Great Respected Prof. you are doing a good job for learners

  • @niamatullahbaloch9358
    @niamatullahbaloch9358 12 วันที่ผ่านมา

    Outstanding lecture, loved it a lot, please keep good work up. Thank you so much

  • @muhammadusama1347
    @muhammadusama1347 12 วันที่ผ่านมา

    amazing video thanks