Genomics and Bioinformatics
Workshop
Dr. Vinayak Mathur, PhD
Assistant Professor
Sep 30th 2024
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Talk Outline
• Journey as a scientist
• Background
• Research project
• Questions
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High School
College
Graduate School …
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Growing up in Dehradun
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Talk Outline
• Journey as a scientist
• Background
• Research project
• Questions
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My research
focusses on the
interaction of
bacteriophages
and bacteria
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Living vs Non-Living
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Are viruses living or non-living?
Argument for living Argument for non-living
• Complexity of structure – • Cannot maintain
contain either DNA or RNA homeostasis
• Evolve and adapt to their • Cannot self-replicate
environment • Cannot grow larger
• Respond to stimuli • Cannot produce own
• Use energy from a host energy
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Bacteriophages
• Found everywhere that
bacteria is present
• Unique host ranges
• Poorly understood
mechanisms by which
these viruses infect
bacteria
• And how these
interactions drive their
Retrieved from:
evolution https://www.google.com/search?q=bacteriophage&rlz=1C1GCEV_enUS860US860&sourc
e=lnms&tbm=isch&sa=X&ved=0ahUKEwjhtrXLiOLjAhXNx1kKHQFSCngQ_AUIESgB
&biw=1260&bih=648#imgrc=Ya1IgyucrnatxM:
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Bacteriophage Life Cycle
Lytic cycle Lysogenic cycle
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Research Questions
What is Horizontal
Gene Transfer?
How do you identify it?
Retrieved from:
https://www.google.com/search?q=bacteriophage&rlz=1C1GCEV_enUS860US860&sourc
e=lnms&tbm=isch&sa=X&ved=0ahUKEwjhtrXLiOLjAhXNx1kKHQFSCngQ_AUIESgB
&biw=1260&bih=648#imgrc=Ya1IgyucrnatxM:
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What is a
coronavirus?
Protein
spikes that
• Coronaviruses are a group of
the virus
uses to
attach to
viruses that cause several
host cells.
diseases in mammals and birds.
• In humans, coronaviruses cause
respiratory infections that are
usually mild, including some cases
of the common cold.
Slide courtesy: Dr. Eric J. Simon
• Some coronaviruses cause
serious diseases in humans.
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Genomic regions of SARS-CoV-2
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Talk Outline
• Journey as a scientist
• Background
• Research project
• Questions
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Materials & Methods: Community Science Project Pipeline
● Start with a phage protein (Example: Major capsid
protein in Microviridae sp.)
● Forward BLAST -> Search against the bacteria database
https://www.ncbi.nlm.nih.gov/BLAST/
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Materials & Methods: Community Science Project Pipeline
● Start with a phage protein (Example: Major capsid
protein in Microviridae sp.)
● Forward BLAST -> Search against the bacteria database
● Assess top ten hits -> Results will be assessed at a level
of an e-value of e-50 or lower and a query coverage of
70% or higher.
● Pick the top hit -> Reverse BLAST -> Search against the
virus database
● Check to see if top hit from Reverse BLAST matches
initial protein searched for
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Phage Accession Numbers: Tail tape measure protein
ASN67947.1 CAB4136021.1 CAB4153403.1
ASN68175.1 CAB4137094.1 ASN69689.1
CAB4121437.1 CAB4151475.1 ASN69545.1
ASN69051.1 CAB4152139.1 ASN69051.1
ASN69758.1 CAB4137255.1 ASN68781.1
ASN70099.1 CAB4187274.1
ASN71960.1
ASN70518.1 CAB4165949.1 CAB4127914.1
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Phage Accession Numbers: ASN68652.1
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After you have identified your bacteria
and bacteriophage pair in HGT you now
have to validate the result
How?
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Validating HGT using Phylogenetics software
Software tool: https://www.phylogeny.fr/
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Validating HGT using Phylogenetics software
Software tool: https://www.phylogeny.fr/
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Talk Outline
• Journey as a scientist
• Background
• Research project
• Questions and Takeaways
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Message for students
• Science is messy, everyone has their own journey
• Mistakes are how we learn
• Perseverance is more important than intelligence
to be successful
• Specific advice: Learn how to code!
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Thank you for listening!
Questions?
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