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Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and
Mahmoud Naghibzadeh1,2, Hossein Savari1, Abdorreza Savadi2
1Knowledge Engineering Research Group, Computer Engineering Dept., Ferdowsi University of Mashhad, Mashhad, Iran.
Informatics in Medicine Unlocked
|June 6, 2020
Summary
This study introduces Fast Microsatellite Discovery (FMSD), a new computational method for identifying microsatellites in viral genomes like SARS and Covid-19. FMSD reveals key genomic differences between these viruses, aiding in understanding their malicious properties.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The Coronavirus-Covid-19 pandemic highlights the need to understand viral genomes for developing treatments and vaccines.
- Microsatellites, repetitive DNA sequences, are highly variable and implicated in various diseases.
- Analyzing the pathogen's genome, rather than the host's, can reveal its specific characteristics.
Purpose of the Study:
- To develop and implement an efficient computational method for identifying microsatellites in viral genomes.
- To analyze and compare microsatellites in SARS and Covid-19 genomes.
- To identify significant genomic differences between SARS and Covid-19.
Main Methods:
- Developed and implemented a novel computer method named Fast Microsatellite Discovery (FMSD).
- FMSD utilizes an efficient K-Mer Hash Indexing technique for rapid microsatellite identification.
- The method was applied to the genome sequences of Coronavirus-Covid-19 and SARS2003.
Main Results:
- Successfully identified all microsatellites in both Coronavirus-Covid-19 and SARS2003 genomes.
- A comprehensive table detailing the identified microsatellites for each virus was generated.
- Significant genomic differences were observed between SARS and Covid-19, with one notable difference requiring further investigation.
Conclusions:
- The Fast Microsatellite Discovery (FMSD) method provides an accurate and efficient means to analyze viral microsatellites.
- Comparative analysis revealed distinct microsatellite profiles between SARS and Covid-19.
- Further research into the identified unique genomic features of Covid-19 is warranted.
