AppIndels

AppIndels identifies taxon-specific conserved signature indels (CSIs) in genome sequences to demarcate taxa molecularly and predict taxonomic affiliation.

Key Features:

• Taxon-Specific CSI Identification: AppIndels detects known conserved signature indels (CSIs) within input genome sequences.
• Curated CSI Database: The database contains 585 validated CSIs used for identification and comparison.
• Broad Taxonomic Coverage: Coverage includes approximately 45 genera within Bacillales and CSIs for members of Neisseriales, Legionellales, Chlorobiales, the family Borreliaceae, and certain species/genera of Pseudomonadaceae.
• Empirical Demonstration: Application to 721 Bacillus strains identified significant numbers of CSIs specific to various Bacillales genera and families.
• Validation via Phylogenomics: Predictions were corroborated by phylogenomic tree reconstructions showing congruent branching with predicted taxa.

Scientific Applications:

• Taxonomic Affiliation Prediction: Detection of CSIs is used to predict the taxonomic affiliation of strains, including those of unknown taxonomy.
• Phylogenomic Analysis Support: CSI presence/absence data can be used to support grouping of strains consistent with phylogenomic trees.
• Diagnostic and Research Marker Identification: CSIs serve as molecular synapomorphies useful for genetic, biochemical, and diagnostic studies.

Methodology:

AppIndels scans genome sequences against a curated database of 585 validated CSIs, identifies the presence of these indels, and uses presence/absence data to predict taxonomic affiliation; predictions were corroborated by phylogenomic tree reconstructions in a study of 721 Bacillus strains.