Genome Sequence Retrieval, Assembly & Quality analysis | WGS-1 | Lecture 423 | Dr. Muhammad Naveed
Genome Sequence Retrieval, Assembly & Quality analysis (NCBI):
Example link: https://www.ncbi.nlm.nih.gov/datasets...
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.
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: https://ucp.edu.pk/member/dr-muhammad...
2. Facebook: / drmuhammadnaveed22
3. LinkedIn: https://www.linkedin.com/in/dr-muhamm...
4. Instagram: / prof.dr.naveed
5. Google Scholar: https://scholar.google.com/citations?...
6. ResearchGate: https://www.researchgate.net/profile/...
7. Twitter: / naveedqau
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