copMEM2

copMEM2 finds Maximum Exact Matches (MEMs) between genomic sequences to enable precise genome-to-genome comparisons.

Key Features:

• Multithreaded implementation: leverages multithreading to increase computational throughput and scalability.
• Predecessor query data structure: employs a predecessor query data structure to improve match-finding performance.
• Adaptive sort procedures: selects sort procedures based on input data characteristics to optimize speed and resource usage.
• Optimization for similar genomes: specifically tuned for comparisons involving very similar genomes, such as human and mouse.
• Benchmark performance: computes all MEMs of minimum length 50 between the human and mouse genomes in 59 seconds using 10.40 GB RAM and 12 threads, and compares human genome versions hg18 and hg19 in 324 seconds with 16.57 GB memory.

Scientific Applications:

• Comparative genomics: facilitates identification of MEMs between highly similar genomes for genome-to-genome comparison.
• Evolutionary analysis: supports inference of evolutionary relationships through conserved exact matches.
• Conserved region detection: aids in locating conserved genomic regions by finding non-extendable exact matches.
• Genomic variation detection: assists detection of genomic variations by highlighting differences in exact-match patterns.

Methodology:

Multithreaded processing, a predecessor query data structure, adaptive sort procedures, and a series of optimizations tailored to handle large-scale and very similar genomic data.