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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2005

Open Access Research article

Browsing Isolated Population Data

Gianmaria Mancosu1*, Massimiliano Cosso1, Francesca Marras1, Cesare Cappio Borlino1, Giuseppe Ledda1, Teresa Manias1, Mauro Adamo1, Donatella Serra1, Paola Melis2 and Mario Pirastu12

Author Affiliations

1 SharDNA Life Sciences, Cagliari, Italy

2 Istituto di Genetica delle Popolazioni, CNR, Alghero (Sassari), Italy

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BMC Bioinformatics 2005, 6(Suppl 4):S17  doi:10.1186/1471-2105-6-S4-S17

Published: 1 December 2005

Abstract

Background

In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships.

To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies.

Results

The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects.

Availability

PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com. webcite