FAME

FAME performs fast and memory-efficient multiple sequence alignment of very long genomic sequences, reducing processing time and memory use while improving sum-of-pair (SP) alignment scores.

Key Features:

• Vertical Division Strategy: Divides sequences at shared/common regions to produce subsequences that are aligned between these common regions.
• Integration with existing MSA methods and minimizers: Aligns subsequences using established MSA tools and leverages minimizers to enhance performance.
• Improved Alignment Scores: Produces higher sum-of-pair (SP) scores compared to standalone MSA tools, with greater gains on longer genomic datasets.
• Computational Efficiency: Reduces memory requirements and accelerates alignment, achieving at least fourfold faster execution on large datasets.
• Scalable long-sequence alignment: Handles genome-sized and very long sequences by reducing processing time and memory consumption.

Scientific Applications:

• Genomics: Performing genome-scale alignments for comparative analyses and large-scale sequence comparisons.
• Evolutionary biology: Supporting analyses of sequence evolution that require long-sequence alignments.
• Phylogenetic studies: Generating alignments used for phylogenetic inference from genome-sized sequences.
• Analysis of genetic variation: Facilitating detection and interpretation of genetic variation across long genomic regions.

Methodology:

Identifying common areas within sequences; arranging these areas consecutively and shifting them to align vertically; aligning the subsequences between these common regions using existing MSA tools; and combining the subsequence alignments to produce a comprehensive alignment.