TY  - JOUR
AB  - Background:

The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps.
Results:

Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step.
Conclusions:

Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.
DA  - 2011
DO  - 10.1186/1471-2105-12-S9-S8
LA  - eng
IS  - Suppl 9: Proc. of RECOMB-CG 2011
PY  - 2011
SN  - 1471-2105
T2  - BMC Bioinformatics
TI  - Genomic distance under gene substitutions
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-23965098
Y2  - 2024-11-24T00:56:35
ER  -