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SegAnnDB: interactive web-based genomic segmentation
- Source :
- Bioinformatics, Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩, Bioinformatics, Oxford University Press (OUP), 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩, Bioinformatics, Oxford University Press (OUP), 2014, 30 (11), pp.1539-1546. 〈10.1093/bioinformatics/btu072〉
- Publication Year :
- 2014
- Publisher :
- HAL CCSD, 2014.
-
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. 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. Contact: toby@sg.cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Source code
DNA Copy Number Variations
media_common.quotation_subject
Chromosome Breakpoints
Gene Expression
SNP
Genomics
Genome browser
Biology
Biochemistry
World Wide Web
Chromosome (genetic algorithm)
Web application
TOOL
Segmentation
[ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Molecular Biology
ComputingMilieux_MISCELLANEOUS
media_common
Internet
Information retrieval
business.industry
ARRAY-CGH DATA
PROFILES
Original Papers
CANCER
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Visualization
Computational Mathematics
COPY NUMBER
Computational Theory and Mathematics
MICROARRAY DATA
VISUALIZATION
business
Algorithms
Software
Subjects
Details
- Language :
- English
- ISSN :
- 13674803, 13674811, and 14602059
- Database :
- OpenAIRE
- Journal :
- Bioinformatics, Bioinformatics, 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩, Bioinformatics, Oxford University Press (OUP), 2014, 30 (11), pp.1539-1546. ⟨10.1093/bioinformatics/btu072⟩, Bioinformatics, Oxford University Press (OUP), 2014, 30 (11), pp.1539-1546. 〈10.1093/bioinformatics/btu072〉
- Accession number :
- edsair.doi.dedup.....40f8522738edae5310eb88273c7e5c54