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Dr. Muhammad Naveed
Pakistan
Приєднався 2 тра 2012
Bioinformatician, Molecular Biotechnologist & Motivational Speaker
Identify Prophage in Bacterial Genome by PHASTEST | WGS-8 | Lecture 429 | Dr. Muhammad Naveed
Identification of Prophage sequences in Bacterial Genome by PHASTEST.
PHASTEST: phastest.ca/
Result (Example):phastest.ca/submissions/ZZ_b385032e0d#!
PHASTEST (PHAge Search Tool with Enhanced Sequence Translation)
is a web server designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports extensive annotation and interactive visualization of all other genes (protein coding regions, tRNA sequences and rRNA sequences) in those same genomes. PHASTEST can now process a typical bacterial genome in 3.2 minutes from the raw sequence alone or in 1.3 minutes when given a pre-annotated GenBank file. PHASTEST is 30.5% faster than PHASTER. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors (PHAST and PHASTER), but it also provides more complete whole genome annotations and much improved genome visualization capabilities. PHASTEST now offers a much more responsive, interactive visualization interface that allows users to generate, edit, annotate and interactively visualize (zooming, rotating, dragging, panning, resetting) publication quality genome maps (both circular and linear versions).
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
#genome #phage #virus #bioinformatics #drmuhammadnaveed
PHASTEST: phastest.ca/
Result (Example):phastest.ca/submissions/ZZ_b385032e0d#!
PHASTEST (PHAge Search Tool with Enhanced Sequence Translation)
is a web server designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports extensive annotation and interactive visualization of all other genes (protein coding regions, tRNA sequences and rRNA sequences) in those same genomes. PHASTEST can now process a typical bacterial genome in 3.2 minutes from the raw sequence alone or in 1.3 minutes when given a pre-annotated GenBank file. PHASTEST is 30.5% faster than PHASTER. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors (PHAST and PHASTER), but it also provides more complete whole genome annotations and much improved genome visualization capabilities. PHASTEST now offers a much more responsive, interactive visualization interface that allows users to generate, edit, annotate and interactively visualize (zooming, rotating, dragging, panning, resetting) publication quality genome maps (both circular and linear versions).
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
#genome #phage #virus #bioinformatics #drmuhammadnaveed
Переглядів: 26
Відео
Genome Flexibility analysis by IslandViewer 4 | WGS-7 | Lecture 428 | Dr. Muhammad Naveed
Переглядів 17316 годин тому
Genome Flexibility or Gene Reprogramming Analysis by IslandViewer 4. IslandViewer 4: www.pathogenomics.sfu.ca/islandviewer/upload/ Result (Example):www.pathogenomics.sfu.ca/islandviewer/accession/NC_017625.1/ IslandViewer Definitions Genomic Islands - large genomic regions typically more than 8kb, that are thought to have horizontal origins. These regions can often contain genes that are relate...
Bacteriocins and AMR genes prediction in Genome | BAGEL4 | ResFinder | WGS-6 | Lec 427 | Dr. Naveed
Переглядів 23214 днів тому
Bacteriocins and AMR genes prediction in Genome by BAGEL4 & ResFinder. BAGEL4: bagel4.molgenrug.nl/ ResFinder: genepi.food.dtu.dk/resfinder Result (Example):cge.food.dtu.dk/services/ResFinderFG/output.php BAGEL enables researchers to mine bacterial (meta-)genomic DNA for bacteriocins and RiPPs. Additionally we provide databases and a BLAST against the core peptide databases. Check out the help ...
Genome comparisons and Exploration | panX | WGS-5 | Lecture 426 | Dr. Muhammad Naveed
Переглядів 26321 день тому
panX: pan-genome analysis and Exploration. panX: pangenome.org/ Results (Example): pangenome.org/Escherichia_coli panX is a software package for comprehensive analysis, interactive visualization and dynamic exploration of bacterial pan-genomes. The analysis pipeline is based on DIAMOND, MCL and phylogeny-aware post-processing. The visualization application encompasses various interconnected com...
Genome Nucleotide identity & Taxonomic Analysis | GGDC | TYGS | WGS-3 & 4 | Lecture 425 | Dr. Naveed
Переглядів 25928 днів тому
Genome Nucleotide Identity & Taxonomic Analysis by GGDC & TYGS GGDC: ggdc.dsmz.de/ggdc.php# TYGS: tygs.dsmz.de/user_requests/new Results (Example): tygs.dsmz.de/user_results/show?guid=38227feb-5883-4624-9a51-ba1d592c6656 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. 1. Genome-Genome Distance ...
Highlights of 6th National Bioinformatics Training Workshop 2024 | UCP | Dr. Muhammad Naveed
Переглядів 476Місяць тому
6th National Hands-on Training workshop on advanced Bioinformatics and Recombinant Biotechnology 21-22 August, 2024 Alhamdulillah, we successfully conducted the 6th National Training Workshop on Bioinformatics and Recombinant Biotechnology, with 100 participants, including professors, researchers, students from across Pakistan, and international researchers. Here are some potential key takeaway...
Genome Assembly & Annotations | GenMark | BV-BRC | PATRIC| WGS-2 | Lecture 424 | Dr. Muhammad Naveed
Переглядів 422Місяць тому
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 ...
Genome Sequence Retrieval, Assembly & Quality analysis | WGS-1 | Lecture 423 | Dr. Muhammad Naveed
Переглядів 680Місяць тому
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
Переглядів 1,6 тис.2 місяці тому
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
Переглядів 8472 місяці тому
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: ua-cam.com/video/GdhC7o9fHpQ/v-deo.html 2. Motivational Letter: ua-cam.com/video/VixhSipDRRU/v-deo.html 3....
University of Melbourne, Australia Scholarships | MS & PhD | Lecture 167 | Dr. Muhammad Naveed
Переглядів 1 тис.2 місяці тому
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
Переглядів 8232 місяці тому
Skoltech Fully Funded Scholarships for Russia | Master program | Lecture 166 | Dr. Muhammad Naveed
Upgrade Your Life Model with New Skills | Lecture 1008 | Dr. Muhammad Naveed
Переглядів 1963 місяці тому
Upgrade Your Life Model with New Skills | Lecture 1008 | Dr. Muhammad Naveed
Focused on Blessings and Ignore Negativity | Lecture 1007 | Dr. Muhammad Naveed
Переглядів 1463 місяці тому
Focused on Blessings and Ignore Negativity | Lecture 1007 | Dr. Muhammad Naveed
Stop Comparing Yourself to Others | Motivational story | Lecture 1006 | Dr. Muhammad Naveed
Переглядів 4123 місяці тому
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
Переглядів 9504 місяці тому
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
Переглядів 4264 місяці тому
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
Переглядів 1,5 тис.5 місяців тому
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
Переглядів 1,3 тис.5 місяців тому
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
Переглядів 6425 місяців тому
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
Переглядів 8965 місяців тому
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
Переглядів 2,9 тис.6 місяців тому
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
Переглядів 2,1 тис.6 місяців тому
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
Переглядів 1,2 тис.6 місяців тому
Perplexity AI | The Academic Writing Choice over ChatGPT | Lecture 115 | Dr. Muhammad Naveed
Pharmit | Pharmacophore based virtual Drug screening | Lecture 114 | Dr. Muhammad Naveed
Переглядів 1,7 тис.6 місяців тому
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
Переглядів 1,9 тис.7 місяців тому
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
Переглядів 9297 місяців тому
GENSCAN | Identification of gene structures in genomic DNA | Lecture 112 | Dr. Muhammad Naveed
PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111 | Dr. Muhammad Naveed
Переглядів 1,6 тис.7 місяців тому
PDBsum | LIGPLOT | Protein-Protein Interactions analysis | Lecture 111 | Dr. Muhammad Naveed
University of Luxembourg Scholarships | Fully funded MS & PhD | Lecture 163 | Dr. Muhammad Naveed
Переглядів 7 тис.8 місяців тому
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
Переглядів 1,1 тис.8 місяців тому
Chief Minister Foreign Ph.D Scholarships | PEEF Fully funded PhD | Lecture 162 | Dr. Muhammad Naveed
Excellent work easy and to the point.
Great job sir
Sir 18 years is the last age so if the age is 19 or 20 it will not be eligible
Sir I have problem in profile picture uploading, my picture is not uploading, even it is of correct size and format
Bilkul basic level pr ja kr ap ne smjhaaya❤❤ Allah ap ko jaza de
outstanding❤❤
Mujhy khoch samj nhi arha kesy shuro karo apny topic ka introduction 😢
Thank you sir
Aslamoalaikum sir... Sir mane freshwater mussels ki collection ki h...our usko ab molecular level pe identify krna h ..tu sir mera question ya ha k (Mane jo specimens collect kiye ha uska tu mere pass koi sequence nhi ha Q k mane find krna ha...pir us k bad may primer design kr skta hu....tu sir kia may ab baqi freshwater mussels ki species ko use kr k primer design kr skta hu manually?...plz guid me sir...
Sir meri beti ki age domicile banany ki age nai hy, i mean wo 21 years ki nai hy or hamen hec scholarship k liy apply krna hy to applicant domicile ki jaga kya upload kren
Thanks❤❤❤
jazakALLAH sir
Please mantion this letter link here
Needed😢
Sir please zroor reply kijiay ga
Assalam-u-alaikum Sir please guide krdyn k Research Assistant ki post k about interview mey kya poocha jaskta ha? Kon se areas pe apko command honi Chahiay to crack your interview? Ur Agr kisi university mey ho interview toh wha kon Leta ha, kya criteria hota ha?
I tried to analyse my PPI network with bingo. But when i opened it in cytoscape, I could not extend it. The start button is below my laptop task bar. I tried to uphold that but couldnot. How can I solve that problem.
Aslam o alikum. Sir how to get acceptance letter from supervisior ? Write reserach purposal and mail to supervisior or what criteria of it. For the masters degree?
its paid?
introduction or literature review k liay ak paper se maximum kitna data ly skty hae hm
Rmsd value sir
AoA sir. Please one lecture on tools that can be used for spa (staphylococcal protein A) typing from Whole genome assembly.
Sir, are you ex aridian
Sir, How can I contact with you?
Sir kindly guide me about hat test preparation material
For Ms chemistry which category of hat should be given?
Jis na BS kia ar MPhil ma is scholarship ka lia apply kr skty hai kia?
Sir will you tell me how to visualize other bonds like salt bridge, pi-pi interaction, van der waal interaction in pymol.. in protein-protein or protein-ligand interaction complex
Sir is great
Sir I am an electrical engineer and doing biomedical engineering in master very difficult course for me
Sir I am using NGS data from SRA NCBI I want to check AMR from CARD but it requires fasta or genbank assession ids where can I find their genbank ID's
❤
Sir EC50 value ko kis in silico software se hum pata kar sakte hain ?
Sir can we change the grid dimensions if we take that protein
Sir Thesis topic ke bare me Literacy article kahan se nikale
Sir plz tell me how can we search introduction reference conclusion
Sir quinoprotein human body protein h?
Sir thank you soo much
Sir how to get the complete genome of any species???
For master's acceptance letter is necessary?
After bsc apply kr sakty ha??
Aap 3 video bus bna dijiye sequence retrieve of pan genome and then how to use proka and roary server and then same process are done like Multi-epitope based vaccine design.
Pan genome based vaccine design me. Virus ke sequence ko yhi se retrieved krna hota kya ya NCBI se hi
Hello sir, please aap proka and roary pe video bnaiye jo ki pan genome based vaccine me used hota hai
Bhai jaan PHD ke liye kehty hain keh 2 years ka job experience ho jis ne master pass hoty hi PHD main admission lena ho toh woh job experience khaan say ley eas ka kiya hall hai main ne kafi logoon ko ye msg kiya koi bhee jwab nahin detta please guide kar dein thanks
Sir how to search the complete genome of any species at NCBI?
Bs k liya nhi ye applicable kiya ?
Can I use it for rna protein docking?
Assalamualaikum Sir Kindly sir WhatsApp number dy dein Research proposal k leye apki help chahy
Recommendation latter agr hum dusre field ke proffessor se krwaie to accept hujaiega? Same university ka hu lekin