Comparative Genomics: Algorithms and Applications

Yang, Xiao; Aluru, Srinivas

doi:10.1002/9780470892107.ch32

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2012

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“…Indeed, preservation of gene co-locality tends to indicate that the corresponding genes either form a functional unit (e.g., operons) or result from speciation or duplication events [12]. In the literature, the former is termed "gene cluster " [3], whereas the latter is known as "synteny" [22]. Both were extensively studied during the past decade, and numerous models and algorithms were proposed to define and identify them.…”

Section: Introductionmentioning

confidence: 99%

An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval

Yang

Sikora

Blin³

et al. 2012

Lecture Notes in Computer Science

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A set of genes that are proximately located on multiple chromosomes often implies their origin from the same ancestral genomic segment or their involvement in the same biological process. Among the numerous studies devoted to model and infer these gene sets, the recently introduced approximate common interval (ACI) models capture gene loss events in addition to the gene insertion, duplication and inversion events already incorporated by earlier models. However, the computational tractability of the corresponding problems remains open in most of the cases. In this contribution, we propose an algorithmic study of a unifying model for ACI, namely Multi-related-segments, and demonstrate that capturing gene losses induces intractability in many cases.

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Section: Introductionmentioning

confidence: 99%