OSTRFPD

OSTRFPD identifies short tandem repeats (STRs) across DNA, transcripts, and amino acid sequences and integrates Primer3 to design microsatellite-targeted primers for marker development.

Key Features:

• Sequence scope: Identifies STRs in DNA, transcripts (RNA), and amino acid sequences.
• Repeat detection: Detects both perfect and imperfect repeats using customizable scoring systems.
• Primer design: Integrates Primer3 to filter flanking regions and generate microsatellite-targeted primers.
• Custom searches: Provides built-in motif-sequence generator engines and supports dictionary mode searches for custom motifs.
• Result outputs: Produces motif categorization, repeat frequencies, densities, coverage, GC content, and text-based imperfect alignment visualizations.
• Implementation: Implemented in Python.

Scientific Applications:

• Genomic STR discovery: Genome-wide identification and cataloging of STRs in DNA sequences.
• Transcript and protein repeat analysis: Analysis of STRs in transcripts and amino acid sequences to study repeat-associated variation.
• Microsatellite marker development: Design and generation of microsatellite-targeted primers for marker development and validation.
• Polymorphism and genotyping studies: Support for polymorphism detection and genotyping via STR profiling and primer design.
• Forensic STR analysis: Application in forensic investigations that require STR profiling.
• Pathogen genomics: Applied to whole-genome analyses of selected Plasmodium species.

Methodology:

OSTRFPD employs an in silico approach to mine STRs, detects perfect and imperfect repeats with customizable scoring, uses motif-sequence generator engines and dictionary mode searches, integrates Primer3 for flanking-region filtering and primer generation, and outputs motif statistics and text-based imperfect alignment visualizations; it has been applied to whole-genome sequences of selected Plasmodium species.