AMID: autonomous modeler of intragenic duplication.

Sarah K. Kummerfeld; Anthony S. Weiss; Alan Fekete; Lars S. Jermiin

AMID: autonomous modeler of intragenic duplication.

Sarah K. Kummerfeld
, Anthony S. Weiss
, Alan Fekete
, Lars S. Jermiin

Sydney University Biological Informatics and Technology Centre (SUBIT)

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

5 Citations (Scopus)

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.

Original language	English
Pages (from-to)	169-176
Number of pages	8
Journal	Applied bioinformatics
Volume	2
Issue number	3
Publication status	Published - 2003
Externally published	Yes

Cite this

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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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AB - 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.

UR - https://www.scopus.com/pages/publications/2642579315

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JO - Applied bioinformatics

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AMID: autonomous modeler of intragenic duplication.

Abstract

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