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AMID: autonomous modeler of intragenic duplication
Authors:Kummerfeld Sarah K  Weiss Anthony S  Fekete Alan  Jermiin Lars S
Institution:School of Molecular and Microbiological Biosciences, University of Sydney, Sydney, NSW, Australia. skk@mrc-lmb.cam.ac.uk
Abstract:Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.
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