Identification of ortholog groups is a crucial step in comparative
analysis of multiple genomes. Although several computational methods
have been developed to create ortholog groups, most of those methods do
not evaluate orthology at the sub-gene level. In our method for
domain-based ortholog clustering,
DomClust
, proteins are split into
domains on the basis of alignment boundaries identified by
all-against-all pairwise comparison, but it often fails to determine
appropriate boundaries.
We developed a method to improve domain-based ortholog classification
using multiple alignment information. This method is based on a scoring
scheme,
the domain-specific sum-of-pairs (DSP) score
, which evaluates
ortholog clustering results at the domain level as the sum total of
domain-based alignment scores. We developed a refinement pipeline to
improve domain-based clustering,
DomRefine
, by optimizing the DSP
score.
v1.1.1 |
README file |