alfy

alfy identifies intervals of local homology between query DNA sequences and subject sequences using an alignment-free comparison based on lengths of exact matches to detect recombination and mosaic structures arising from horizontal gene transfer.

Key Features:

• Alignment-free exact-match length comparison: Compares lengths of exact matches between sequence pairs to infer local homology without performing sequence alignment.
• Local homologue interval identification: Identifies intervals that indicate the closest homologues among query and subject sequence sets by classifying long matches as close homology and short or absent matches as distant or none.
• Enhanced suffix array lookup: Uses an enhanced suffix array to efficiently look up exact match lengths for rapid processing of large genomic datasets.
• Recombination breakpoint detection: Detects recombination breakpoints in simulated DNA sequences and among recombinant strains, including analyses of HIV-1.
• Application to bacterial genomes: Applied to bacterial genomes, notably Escherichia coli, to detect mosaic genome structures related to horizontal gene transfer and pathogenicity.
• Implementation: Implemented in standard C and released under the GNU General Public License.

Scientific Applications:

• Medical Microbiology: Identification of unique genomic regions potentially linked to virulence to study mechanisms of pathogenicity and transmission.
• Genomic Research: Detection of mosaic structures and recombination events for evolutionary studies and comparative genomics.
• Public Health: Analysis of zoonotic and infectious pathogens to inform monitoring and control strategies based on genomic signatures of transfer and recombination.

Methodology:

Compares query DNA sequences to subject sequences by computing lengths of exact matches using an enhanced suffix array, identifying intervals of closest homology and classifying match-length patterns to detect recombination breakpoints (applied to simulated sequences, recombinant strains such as HIV-1, and bacterial genomes including Escherichia coli).