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Updated: May 3, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
SegAnnDB: interactive Web-based genomic segmentation
Toby D Hocking1, Valentina Boeva2, Guillem Rigaill1
1Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8552, Japan, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, INSERM U900, Paris F-75248, France, Mines ParisTech, Centre for Computational Biology, 77300 Fontainebleau, Unité de Recherche en Génomique Végétale INRA-CNRS-Université d'Evry Val d'Essonne, Évry 91057, France, INSERM U830, Paris F-75248, France, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya-city 464-8681, Japan and INRIA-Sierra Project-Team, Département d'Informatique de l'École Normale Supérieure, Paris F-75013, France.
Motivation:
DNA copy number profiles characterize regions of chromosome gains, losses and breakpoints in tumor genomes. Although many models have been proposed to detect these alterations, it is not clear which model is appropriate before visual inspection the signal, noise and models for a particular profile.
Results:
We propose SegAnnDB, a Web-based computer vision system for genomic segmentation: first, visually inspect the profiles and manually annotate altered regions, then SegAnnDB determines the precise alteration locations using a mathematical model of the data and annotations. SegAnnDB facilitates collaboration between biologists and bioinformaticians, and uses the University of California, Santa Cruz genome browser to visualize copy number alterations alongside known genes.
Availability And Implementation:
The breakpoints project on INRIA GForge hosts the source code, an Amazon Machine Image can be launched and a demonstration Web site is http://bioviz.rocq.inria.fr.
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