SimpleSynteny

SimpleSynteny visualizes microsynteny among orthologous gene clusters across multiple species to assess local genomic collinearity and infer evolutionary relationships.

Key Features:

• FASTA input: Accepts FASTA-formatted genome and gene sequences for specified gene targets.
• Iterative analysis: Implements an iterative analysis workflow that permits customization of individual genomes prior to integration into combined synteny visualizations.
• Contig identification: Includes tools to identify contigs containing targeted genes.
• Circular genome optimization: Provides methods to optimize synteny analyses for circular genomes.
• Targeted synteny evaluation: Evaluates synteny for preselected gene targets across multiple genomes.
• High-resolution visualization: Produces high-resolution visualizations of local syntenic regions and genomic collinearity across species.

Scientific Applications:

• Comparative genomics: Facilitates studies of organismal evolution by assessing local gene-order conservation across species.
• Microsynteny analysis: Enables targeted interrogation of local genomic neighbors' collinearity in orthologous gene clusters to investigate genomic organization and evolutionary relationships.

Methodology:

Implements a pipeline to evaluate synteny of preselected gene targets across multiple genomes using FASTA-formatted genome and gene sequences and an iterative process for customization and visualization of syntenic regions.