SegAnnDB: interactive web-based genomic segmentation - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Bioinformatics Year : 2014

SegAnnDB: interactive web-based genomic segmentation

Abstract

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.
Fichier principal
Vignette du fichier
btu072.pdf (546.25 Ko) Télécharger le fichier
Origin Publisher files allowed on an open archive

Dates and versions

hal-01101868 , version 1 (29-01-2024)

Identifiers

Cite

Toby D. Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, et al.. SegAnnDB: interactive web-based genomic segmentation. Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩. ⟨hal-01101868⟩
313 View
5 Download

Altmetric

Share

Gmail Mastodon Facebook X LinkedIn More