Terrapon N, Grath S, Weiner J, Moore AD and Bornberg-Bauer E
Fast Homology Search Using Domain-Architecture Alignment
JOBIM, Conference proceedings, 2012

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Homology detection, i.e. the identification of genes that share common ancestry, is key
to understanding the evolutionary history of gene families. However, homology detection using
local sequence similarity alone (such as employed by BLAST) can be problematic when applied to
multi-domain proteins, as true homology can be masked by local similarity of domain sequences.
Here, we present a new approach for detecting homology that is based on the global alignment
of domain arrangements. It combines the ability of global alignments to capture homology across
the entire sequence with the efficiency and sensitivity of local alignments.
A web-based interface is available under http://rads.uni-muenster.de .