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Related Experiment Video

Updated: Feb 2, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Block alignment: New representation and comparison method to study evolution of genomes.

Hossein Lanjanian¹, Abbas Nowzari², Nazanin Hosseinkhan¹

¹Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

|November 17, 2018

Summary

Natural selection shapes genomes, not random sequences. A new Block Alignment method compares genomes using nucleotide counts in blocks, simplifying analysis and reducing sequencing costs for faster, accurate phylogenetic and disease-related genomic comparisons.

Keywords:

Adaptable Block alignment Alignment confirmation algorithm Binary tree Block alignment Comparison Phylogenetic network Similarity network

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Biological sequences are shaped by natural selection, not random processes.
Existing genome comparison methods can be computationally intensive and costly due to high-coverage sequencing requirements.

Purpose of the Study:

To develop a novel, efficient method for genome comparison.
To introduce a similarity score and distance metric based on subsequence nucleotide counts.
To demonstrate the utility of the method in phylogenetic analysis and disease-related genomic studies.

Main Methods:

The Block Alignment method compares genomes by analyzing nucleotide counts within subsequences (blocks), disregarding exact sequence order.
This approach bypasses the need for high-coverage sequencing by excluding point mutations and small variations.
The method enables faster sequence comparisons and identification of conserved blocks.

Main Results:

Phylogenetic trees constructed using Block Alignment for bacterial genomes showed strong agreement with established trees.
Inferred similarity networks revealed community structures consistent with phylogenetic clades, indicating inherent phylogenetic information.
The method successfully distinguished between different types of iAMP21 rearrangements in acute lymphoblastic leukemia by analyzing chromosome 21 subgroups.

Conclusions:

The Block Alignment method offers a computationally efficient and cost-effective approach to genome comparison.
This method retains significant phylogenetic information and can be applied to various genomic analyses, including disease subtyping.
The model's ability to identify conserved blocks facilitates more targeted and accurate downstream analyses.