Predicting Type-I (Rate-Shift) Functional Divergence of Protein Sequences and Applications in Functional Genomics

Authors: Gu, Xun¹; Wang, Yufeng¹; Gu, Jianying¹; Velden, Kent V.¹; Xu, Dongping¹

Source: Current Genomics, Volume 7, Number 2, April 2006 , pp. 87-96(10)

Publisher: Bentham Science Publishers

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Abstract:

Functional divergence after gene duplications is a fundamental issue for functional innovations in many organisms. As gene family proliferation (gene duplication) may have provided the raw materials for the origin of new genes, the details of how duplicate genes have preserved through functional divergence remain largely unknown. In this review paper, we discuss some recent developments about this important issue, with special references to the implication for functional genomics. With a combination of large-scale genome sequencing and powerful computational analysis, we show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The software DIVERGE can be obtained form http://xgu.gdcb.iastate.edu.

Keywords: Vertebrate Mitochondrial Genomes; Amino Acid Residues; JAK Proteins; Mitochondria Genes; caspases; Cluster-Specific Functional Divergence

Document Type: Research article

DOI: 10.2174/138920206777304623

Affiliations: 1: Iowa State University, 536 Science II Hall, Ames, IA 50011, USA.

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