AutomAted RepeaT Identifier (AARTI): A tool to identify common, polymorphic, and unique microsatellites.

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Microsatellites, or simple sequence repeats (SSRs), are valuable genetic markers due to their abundance and polymorphism.
• Existing tools lack the ability to identify common, polymorphic, and unique microsatellites between paired nucleotide sequences.
• Comparative genomic studies require efficient methods for microsatellite analysis.

Purpose of the Study:

• To develop an automated computational pipeline for identifying common, polymorphic, and unique microsatellites.
• To provide a tool that enables pairwise comparison of microsatellites across nucleotide sequences.
• To facilitate comparative genomic analyses and studies of microsatellite length variation.

Main Methods:

• Development of a fully automated computational pipeline named AutomAted RepeaT Identifier (AARTI).
• Pipeline constructed using PERL, with a web server developed using PHP, HTML, CSS, and JavaScript.
• Tested on 7 mitochondrial genomes of the genus Orthotrichum and applied to 5846 Metazoa and 130 Viridiplantae mitochondrial genomes.

Main Results:

• AARTI successfully identifies common, polymorphic, and unique microsatellites between sequence pairs.
• The pipeline reproduced results from a previous study on Orthotrichum mitochondrial genomes.
• Demonstrated application on a large dataset of mitochondrial genomes from Metazoa and Viridiplantae.

Conclusions:

• AARTI is the first tool capable of identifying common, polymorphic, and unique microsatellites between any pair of nucleotide sequences.
• The pipeline will accelerate studies on microsatellite length variation and comparative genomics.
• AARTI is freely available and has the potential for routine genome analysis, particularly for mitochondrial genomes.