GRAMEP

GRAMEP identifies single nucleotide polymorphisms (SNPs) in DNA sequences from assembled genomes using an alignment-free approach based on the maximum entropy principle.

Key Features:

• Alignment-free SNP identification: Discovers informative k-mers specific to a genome or set of sequences without sequence alignment.
• Maximum entropy principle: Adopts the principle of maximum entropy to identify the most informative k-mers for detecting variant-specific mutations.
• Reference-based comparison: Enables detection of variant-specific mutations in comparison to a reference genome or other set of sequences.
• Novel sequence classification: Offers classification of novel sequences without requiring organism-specific information.
• High accuracy with lower computational cost: Demonstrates high accuracy in SNP identification while maintaining lower computational cost compared to alignment-based methods.

Scientific Applications:

• Viral genome analysis: Accurately identifies variants in viral genomes including Dengue, HIV, and SARS-CoV-2.
• SARS-CoV-2 variant identification: Maintains accurate identification of SARS-CoV-2 variants.
• In silico simulation validation: Demonstrates high accuracy in computational simulations of genomic data.
• Genomic mutation investigation: Supports analysis of genomic mutations relevant to chromosomal evolution, genetic disorders, and diseases.

Methodology:

GRAMEP adopts the principle of maximum entropy to discover informative k-mers specific to a genome or set of sequences, which enable the detection of variant-specific mutations in comparison to a reference genome or other set of sequences.