Flexible case-based retrieval for comparative genomics

Authors:
Stefania Montani;Giorgio Leonardi;Stefano Ghignone;Luisa Lanfranco
Affiliations:
DISIT--Computer Science Institute, University of Piemonte Orientale, Alessandria, Italy;DISIT--Computer Science Institute, University of Piemonte Orientale, Alessandria, Italy;IPP--CNR, UAS Torino, Turin, Italy;IPP--CNR, UAS Torino, Turin, Italy and Department of Life Science and Systems Biology, University of Turin, Turin, Italy
Venue:
Applied Intelligence
Year:
2013

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Abstract

Comparative genomics represents a key instrument to discover or validate phylogenetic relationships, to give insights on genome evolution, and to infer metabolic functions of a given organism. A tool for properly supporting comparative genomics is of paramount importance in several application domains.We have developed a tool for supporting customized comparative genomics searches. The tool is based on the retrieval step of the Case-Based Reasoning methodology. It takes advantage of an abstraction technique similar to Temporal Abstractions, thus allowing us to neglect irrelevant details.By means of our tool, retrieval is made flexible by the use of abstractions, and efficient by the use of proper taxonomic index structures. Moreover, end-users are allowed to progressively relax or refine their queries in an interactive way. The tool functionalities are exemplified referring to the study of endobacteria living in arbuscular mycorrhizal fungi.