Publication Date

Spring 2026

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)

Department

Computer Science

First Advisor

Dr. Philip Heller

Second Advisor

Dr. Laura Miller Conrad

Third Advisor

Dr. Wendy Lee

Keywords

Assembly, Colistin adjuvants, ArnA, CATwalk, SPAdes, BLAST

Abstract

Research into colistin adjuvants has identified interactions between a host of proteins and proteins found within certain strains of bacteria. BLAST, a widely adopted local sequence alignment tool, was used to create a database containing the genomes of relevant bacterial strains, which would then be used to query against the previously identified proteins. Many of these strains do not have publicly available assemblies, which makes database construction difficult. CATwalk, a new naïve fragment extender, is first described in this paper and used to extend fragments of interest. BLAST results first identified short fragments with sufficient similarity, which can then be extended with CATwalk for further alignment. CATwalk was ultimately unsuccessful in accurately extending the sequence of interest. SPAdes, a well-known greedy assembly algorithm, was used afterwards to create rough assemblies of relevant bacterial genomes. Compelling similarities between ArnA and an unknown protein in K. pneumoniae 0479 were then uncovered. This study provides a new avenue for ongoing research into counteracting colistin resistance in pathogenic bacteria.

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