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Analyzing the Relationship Between Phages and Bacteria Using Protein Sequencing

Nipun Das

August 6th, 2021

Su Lab

Dr. Andrew Su

Dr. Lisa Racki

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Su Lab (sulab.org)

  • Biology Research in the field of Bioinformatics
    • Computer Science, Statistics
  • Creating tools that help crowdsource and organize biomedical data
    • BioGPS
    • Gene Wiki
    • Mark2Cure

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My Project

  • Phages
    • Lysis vs. Lysogeny
  • NAPS
    • Chromatin structural proteins
  • Bacteria fight back

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My Project (continued)

  • Bacterial immune system
    • H-NS proteins
  • Phage homologue
  • Goal: Identify phages that can stop the spread of the silencing proteins of bacteria for further analysis

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ROK Silencing Proteins

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BlastP

  • Input: protein sequences
  • Locates best matches
  • Database: Non-redundant protein sequences
  • Bacillus bacteria

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PhagesDB

  • Database of Actinobacteriophages
  • Comes with a BLASTP tool

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NCBI Virus

  • 3 million sequences of caudovirales
  • 14 million sequences total

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HMMER

  • Tool that creates a profile instead of a single sequence for searches
  • Example profile:

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Positive Control

  • Used the original ROK protein sequences as positive controls
  • Could be improved

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Results

Positive Control

Other Hits (phages)

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Example alignments

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Next Steps

  • Finding more ROK protein data
    • Bacillus
  • Explore other silencing protein families

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Acknowledgements

  • Scripps Research Institute
  • Su Lab
  • Dr. Andrew Su
  • Dr. Lisa Racki
  • Dr. Fangwei Si
  • Jordan Beach
  • Whitney Wagner
  • Dr. Ashok Deniz