title: AMID: autonomous modeler of intragenic duplication.
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.
authors.affiliation: School of Molecular and Microbiological Biosciences, University of Sydney, Sydney, NSW, Australia. skk@mrc-lmb.cam.ac.uk
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Kummerfeld
authors.forename: Anthony S
authors.initials: AS
authors.lastname: Weiss
authors.forename: Alan
authors.initials: A
authors.lastname: Fekete
authors.forename: Lars S
authors.initials: LS
authors.lastname: Jermiin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D016247:Information Storage and Retrieval; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins