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SnoopCGH: software for visualizing comparative genomic hybridization data

J. Almagro-Garcia, M. Manske, C. Carret, S. Campino, S. Auburn, B. L. MacInnis, G. Maslen, A. Pain, C. I. Newbold, D. P. Kwiatkowski, T. G. Clark
2009 Bioinformatics  
We have developed a software tool for SV analysis using data from array CGH technologies, which is also amenable to short-read sequence data.  ...  Array-based comparative genomic hybridization (CGH) technology is used to discover and validate genomic structural variation, including copy number variants, insertions, deletions and other structural  ...  Array comparative genomic hybridization (CGH) is a powerful tool for identifying copy number variation between DNA samples.  ... 
doi:10.1093/bioinformatics/btp488 pmid:19687029 pmcid:PMC2759554 fatcat:mdt3sbulvbbflktzfkwgrwrgry

Genovar: a detection and visualization tool for genomic variants

Kwang Jung, Sanghoon Moon, Young Kim, Bong-Jo Kim, Kiejung Park
2012 BMC Bioinformatics  
None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment.  ...  The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files.  ...  Acknowledgements This work was supported by a grant from Korea Centers for Disease Control and Prevention (4845-301) and intramural grants from the Korea National Institute of Health (2011-N72001-00, 2008  ... 
doi:10.1186/1471-2105-13-s7-s12 pmid:22594998 pmcid:PMC3348018 fatcat:vuhz6pxuujgvfosmsg2penp2ri

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
Results: We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context.  ...  These features make the software especially suitable for the needs of life scientists. Conclusions: FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data.  ...  In the following we will use the term array CGH (array comparative genomic hybridization) as a synonym for methods generating copy number data including classical array CGH tiling microarrays or SNP microarrays  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer

Raj Chari, Kelsie L. Thu, Ian M. Wilson, William W. Lockwood, Kim M. Lonergan, Bradley P. Coe, Chad A. Malloff, Adi F. Gazdar, Stephen Lam, Cathie Garnis, Calum E. MacAulay, Carlos E. Alvarez (+1 others)
2010 Cancer Metastasis Review  
Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape.  ...  As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and  ...  SnoopCGH: software for visualizing comparative genomic hybridization data. Bioinformatics. 2009; 25(20): 2732-2733. [PubMed: 19687029] 90. 2004; 5:13. [PubMed: 15040819] 92.  ... 
doi:10.1007/s10555-010-9199-2 pmid:20108112 pmcid:PMC3415277 fatcat:js2mys5m7rhulmwi3a5ncrf3h4