Phobos

Phobos detects tandem repeats, including microsatellites (MSs) and minisatellites, in genomic sequences to support marker identification and primer design for genetic mapping, population genetics, and forensic analyses.

Key Features:

• Tandem repeat detection: Identifies perfect and imperfect microsatellites (MSs) and minisatellites, including repeat unit sizes exceeding 5000 base pairs.
• Repeat-type discrimination: Distinguishes between different types of tandem repeats for targeted analyses.
• Two-step detection workflow: Performs separate repeat detection steps for masking repetitive regions during sequencing read assembly and for identifying microsatellite candidate loci for primer design.
• Primer design via PRIMER3: Integrates PRIMER3 to design flanking primers for candidate loci and to support selection of primer pairs for multiplex amplifications.
• Integration with STADEN: Operates as an extension within the STADEN package to integrate into sequence analysis workflows.
• Data storage: Stores analysis results in an SQLite database for programmatic access and retrieval.
• Customizable search and output: Provides adjustable search settings and output formats for tailored analyses.

Scientific Applications:

• Microsatellite marker development: Enables high-throughput identification of microsatellite loci and design of flanking primers for marker development projects.
• Genetic mapping: Supports selection of repeat markers and primer pairs suitable for linkage and mapping studies.
• Population genetics: Facilitates discovery of variable tandem repeats for population structure and diversity analyses.
• Forensic genetics: Provides identification of repeat loci and primer design relevant to forensic marker selection.

Methodology:

Tandem repeat detection algorithms identify perfect and imperfect microsatellites and minisatellites (units >5000 bp); two detection steps are used for masking repetitive regions during sequencing read assembly and for identifying candidate loci for primer design; PRIMER3 is used for flanking primer design and selection of primer pairs for multiplexing; results are recorded in an SQLite database.