Recombinations, chains and caps: resolving problems with the DCJ-indel model

Algorithms Mol Biol. 2024 Feb 27;19(1):8. doi: 10.1186/s13015-024-00253-7.ABSTRACTOne of the most fundamental problems in genome rearrangement studies is the (genomic) distance problem. It is typically formulated as finding the minimum number of rearrangements under a model that are needed to transform one genome into the other. A powerful multi-chromosomal model is the Double Cut and Join (DCJ) model.While the DCJ model is not able to deal with some situations that occur in practice, like duplicated or lost regions, it was extended over time to handle these cases. First, it was extended to the DCJ-indel model, solving the issue of lost markers. Later ILP-solutions for so called natural genomes, in which each genomic region may occur an arbitrary number of times, were developed, enabling in theory to solve the distance problem for any pair of genomes. However, some theoretical and practical issues remained unsolved. On the theoretical side of things, there exist two disparate views of the DCJ-indel model, motivated in the same way, but with different conceptualizations that could not be reconciled so far. On the practical side, while ILP solutions for natural genomes typically perform well on telomere to telomere resolved genomes, they have been shown in recent years to quickly loose performance on genomes with a large number of contigs or linear chromosomes. This has been linked to a particular technique, namely capping. Simply put, capping circularizes linear chromosomes by...
Source: Algorithms for Molecular Biology : AMB - Category: Molecular Biology Authors: Source Type: research