Whole Genome Sequence (WGS) analysis | Overview Bacterial Genome | Lecture 422 | Dr. Muhammad Naveed

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.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.
5. Functional Annotation:
Assign functions to predicted genes by comparing them to protein databases like NCBI’s NR, Swiss-Prot, or Pfam using tools like BLAST, HMMER, or InterProScan.
Identify conserved domains and motifs within proteins using databases like Pfam, SMART, or CDD.
6. Annotation of RNA Genes:
Identify ribosomal RNA (rRNA) and transfer RNA (tRNA) genes using tools like RNAmmer or tRNAscan-SE.
Predict other non-coding RNAs using specialized tools and databases like Rfam.
7. Pathway and Metabolic Annotation:
Map genes to metabolic pathways using databases like KEGG, BioCyc, or MetaCyc.
8. Annotation of Regulatory Elements:
Identify promoters, terminators, and other regulatory elements using tools like BPROM, ARNold, or databases like RegPrecise.
9. Quality Assessment:
Validate the accuracy and completeness of the genome annotation using tools like QUAST or BUSCO.
Check for the presence of common bacterial genes and overall genome coverage.
10. Submission to Databases:
Submit the annotated genome to public databases like GenBank, EMBL, or DDBJ for public access and further research.
These steps are iterative and may require multiple rounds of refinement to achieve a high-quality genome annotation.
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, 9060 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:
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7. Twitter: / naveedqau
#wgs #genome #bacteria #annotations #bioinformatics #drmuhammadnaveed

[@afifaisrar1318]

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

[@rameeshaabid7329]

Long awaited series.

[@Prof.Dr.MuhammadNaveed]

pleasures

[@duckgoose2002]

Thanks for this series. I am eager to learn whole Genome sequence.

[@Prof.Dr.MuhammadNaveed]

glad to hear

[@Hammadhussain-j6z]

Thanks for this series

[@Prof.Dr.MuhammadNaveed]

welcome

[@niazbahadar444]

Thank you sir Very informative lecture

[@rameeshaabid7329]

Please also make lecture series on NGS data analysis, alpha and beta diversity analysis.

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@muhammadsalmanfarid8115]

Dear Teacher,
Thank you for this series. Recently, Our lab find new strains of lactobacillus. We have received Whole Genome Sequence data from company as well. They performed different bioinformatics analysis as well.
But I am unable to understand the WGS data and all bioinformatics analysis results and how can I utilize them further.
Please share insights about how can we process this data which we obtained from Company for further study not only the NCBI retrieve sequence data.
Later, Please also guide about how to use these data in research paper preparation as well.
Please upload this series as early as possible. I need it urgently because I have limited time to do all these things. Humble request. Thanks!

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@SohailTheMicrobiologist]

Thank you for this video. Could you please make a video on how to submit the whole genome sequence on the NCBI portal?
also make video on different tools used for WGS analysis the non-redundant protein database (Nr), gene ontology (GO), ), eggNOG, Pfam, SwissProt, TrEMBL

[@Prof.Dr.MuhammadNaveed]

sure

[@farihajavaid4653]

Aoa sir thanks for this series ...kindly make video on NGS data analysis too...and R as well
Sir kindly share how can we utilize all this data analysis (WGS) for writing paper....please we need your guidance..Regards

[@Prof.Dr.MuhammadNaveed]

sure and i have many articles on WGS and search by my name

[@user-tn5zs6qj4x]

Please how to use bioedit to alignment protein

[@Prof.Dr.MuhammadNaveed]

already shared lecture on it