Genome Flexibility or Gene Reprogramming Analysis by IslandViewer 4.
IslandViewer 4: https://www.pathogenomics.sfu.ca/islandviewer/upload/
Result (Example):https://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 related to antibiotic resistance or virulence.
This web site was developed so that researchers could easily view and download genomic islands for all published sequenced bacterial and archaeal genomes that have been predicted using the the currently most accurate GI prediction methods. Users can also upload their own unpublished genomes for analysis. The source code and entire GI data sets are available for download and acknowledgement information is available for those who use our resources.
Sequence Composition GI Prediction Methods - bacterial genomes tend to naturally have differences in sequence composition such as GC% and codon bias. Therefore, a region within a genome that has abnormal sequence composition could indicate that it originated from another genome. Various tools (incl. SIGI-HMM and IslandPath-DIMOB) look for regions with abnormal sequence composition.
Comparative Genomic GI Prediction Methods - genomic regions that are not present within related strains suggest that the region was horizontally transferred. IslandPick is a method that automatically selects comparison genomes that are within a proper evolutionary distance and identifies regions that are unique to only a single genome.
Mobility Genes - are genes related to the movement of mobile genetic elements (incl. genomic islands), such as transposases and integrases.
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-naveed/
2. Facebook: https://www.facebook.com/drmuhammadnaveed22
3. LinkedIn: https://www.linkedin.com/in/dr-muhammad-naveed-7324b534/?originalSubdomain=pk
4. Instagram: https://www.instagram.com/prof.dr.naveed/
5. Google Scholar: https://scholar.google.com/citations?user=fuEwn1cAAAAJ&hl=en
6. ResearchGate: https://www.researchgate.net/profile/Muhammad-Naveed-59
7. Twitter: https://twitter.com/naveedqau
#genome #flexibility #resistance #bioinformatics #drmuhammadnaveed