SplitTester: software to identify domains responsible for functional divergence in protein family

Background: Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family. Results: Our software, SplitTester, takes a multiple protein sequences alignment as input, generated from protein members of two subgroups with known functional divergence. SplitTester was designed to construct the neighbor joining tree (a split cluster) from variable-sized sliding windows across the alignment in a process called split-clustering. SplitTester identifies the regions, whose split cluster is consistent with the functional split, but may be inconsistent with the phylogeny of the protein family. We hypothesize that at least some number of these...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Xiang Gao, Kent Vander Velden, Daniel F. Voytas, Xun Gu
• Keywords: BMCBI 2005, Functional Divergence, Functional Split, Protein