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Restricted DCJ-indel model: sorting linear genomes with DCJ and indels.

Poly H da Silva¹, Raphael Machado, Simone Dantas

¹IME, Universidade Federal Fluminense, Niterói, Brazil. poly.hannah@gmail.com

BMC Bioinformatics

|January 4, 2013

Summary

This study introduces a restricted double-cut-and-join (DCJ) indel model for sorting linear genomes with unequal content. A new algorithm provides a tight upper bound for the genomic distance under these specific evolutionary constraints.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The double-cut-and-join (DCJ) model is a framework for genome sorting, accommodating various mutations like inversions and translocations.
The restricted DCJ model is suitable for linear genomes, requiring immediate reincorporation of newly created circular chromosomes.
Genomes with unequal content necessitate considering insertions and deletions (indels) alongside DCJ operations.

Purpose of the Study:

To analyze the restricted DCJ-indel model for sorting linear genomes with differing genetic content.
To develop a genome sorting algorithm under the restricted DCJ-indel model.
To establish a precise upper bound for the genomic distance within this model.

Main Methods:

Development of a genome sorting algorithm tailored to the restricted DCJ-indel model.
Analysis of DCJ operations and indels with a constraint on circular chromosome reincorporation.
Derivation of a tight upper bound for the restricted DCJ-indel distance.

Main Results:

A novel sorting algorithm for the restricted DCJ-indel model was developed.
A tight upper bound for the restricted DCJ-indel distance was determined.
The study focused on linear genomes with unequal content.

Conclusions:

A tight upper bound for the restricted DCJ-indel distance has been established.
The question of whether this bound equals the general DCJ-indel distance remains an open area for future research.