Abstract

Biopython is a specialized Python tool for computational molecular biology. Various computational molecular analysis that can be performed using Biopython, such as reconstructing phylogenetic trees, multiple sequence analysis, generating complementary sequences, counting amino acids, etc. This technical notes paper describes in detail the procedures computational DNA sequence analysis using Biopython. The DNA polymerase I (polA) gene sequences of bacteria were used in this study to compare the differences between Thermophilic, Mesophilic, and Psychrophilic bacteria.

Highlights

  • Computational biology in the 21st century is growing rapidly, reaching almost all areas of biological sciences. (Markowetz, 2017) said that “all biology is computational biology”, biological knowledge nowadays is analyzed, defined, organized, and accessed through computation

  • The DNA polymerase I gene sequences of bacteria were used in this study to compare the differences between Thermophilic, Mesophilic, and Psychrophilic bacteria

  • The results (Table 2 and Figure 6) show that the thermophilic bacterial group consisting of Thermus thermophilus and Geobacillus stearothermophilus have the highest GC-content of DNA polymerase I gene with 67.86% and 55.21% respectively

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Summary

INTRODUCTION

Computational biology in the 21st century is growing rapidly, reaching almost all areas of biological sciences. (Markowetz, 2017) said that “all biology is computational biology”, biological knowledge nowadays is analyzed, defined, organized, and accessed through computation. DNA polymerase I (polA) gene sequences of several bacterial species from different groups in order to understand the characteristic differences between them genetically, as there are several bacterial species with capability to survive in extremes of temperature and pressure Based on their ability to survive in an environment with a certain temperature range, bacteria can be classified into 3 three groups, namely Thermophilic, Mesophilic, and Psychrophilic (Chen & Berns, 1980; Shing et al, 1975). T. aquaticus is a bacterium that lives in hot springs and hydrothermal vents, this is the reason that Taq polymerase is an enzyme that is tolerant of high temperatures This technical notes paper describes in detail the procedures computational DNA sequence analysis using Biopython. The DNA polymerase I (polA) gene sequences of bacteria were used in this study to compare the differences between Thermophilic, Mesophilic, and Psychrophilic bacteria

DNA SEQUENCE ANALYSIS USING BIOPYTHON
DNA Comparison
Shewanella putrefaciens
Arcobacter butzleri
Findings
CONCLUSION
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